Chebi Tools

Configuration File: chebi_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

ChEBI_get_compound (Type: ChEBITool)

Get detailed information about a chemical entity from ChEBI (Chemical Entities of Biological Inte…

ChEBI_get_compound tool specification

Tool Information:

  • Name: ChEBI_get_compound

  • Type: ChEBITool

  • Description: Get detailed information about a chemical entity from ChEBI (Chemical Entities of Biological Interest) by its CHEBI ID. Returns the compound name, definition, synonyms, molecular formula, mass, InChIKey, SMILES, charge, and star rating (curation quality: 3=manually curated, 2=checked, 1=unchecked). ChEBI is maintained by EBI and is the standard reference for small molecules in biology. Example: CHEBI:15365 returns acetylsalicylic acid (aspirin).

Parameters:

  • chebi_id (integer) (required) ChEBI numeric identifier (without the ‘CHEBI:’ prefix). Examples: 15365 (aspirin), 17234 (glucose), 16236 (ethanol), 15377 (water), 17790 (methanol).

Example Usage:

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

ChEBI_get_ontology_children (Type: ChEBITool)

Get the ontology children (is-a, has-part, has-functional-parent, etc.) of a ChEBI compound. ChEB…

ChEBI_get_ontology_children tool specification

Tool Information:

  • Name: ChEBI_get_ontology_children

  • Type: ChEBITool

  • Description: Get the ontology children (is-a, has-part, has-functional-parent, etc.) of a ChEBI compound. ChEBI uses a rich ontology with relationships like ‘is a’, ‘has part’, ‘has role’, ‘has functional parent’, and ‘is conjugate base/acid of’. This enables navigation of the chemical classification hierarchy. Example: CHEBI:15365 (aspirin) children include NCX-4040 (has functional parent), acetylsalicylate (conjugate base), and Yosprala (has part).

Parameters:

  • chebi_id (integer) (required) ChEBI numeric identifier (without ‘CHEBI:’ prefix). Examples: 15365 (aspirin), 17234 (glucose), 16236 (ethanol).

Example Usage:

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

ChEBI_search (Type: ChEBITool)

Search the ChEBI database for chemical entities by name, formula, or keyword. Uses Elasticsearch-…

ChEBI_search tool specification

Tool Information:

  • Name: ChEBI_search

  • Type: ChEBITool

  • Description: Search the ChEBI database for chemical entities by name, formula, or keyword. Uses Elasticsearch-powered full-text search across compound names, synonyms, definitions, and formulas. Returns matching compounds with IDs, names, formulas, masses, and structures. ChEBI contains 195,000+ chemical entities of biological interest. Example: searching ‘glucose’ returns D-glucose (CHEBI:17234), L-glucose, and related compounds.

Parameters:

  • query (string) (required) Search query string - compound name, synonym, formula, or keyword. Examples: ‘glucose’, ‘caffeine’, ‘C9H8O4’ (aspirin formula), ‘kinase inhibitor’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return. Default: 10. Max: 100.

Example Usage:

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