Aopwiki Tools#

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

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

Available Tools#

AOPWiki_get_aop (Type: AOPWikiDetailTool)#

Get detailed information about a specific Adverse Outcome Pathway (AOP) from AOPWiki by AOP ID. R…

AOPWiki_get_aop tool specification

Tool Information:

  • Name: AOPWiki_get_aop

  • Type: AOPWikiDetailTool

  • Description: Get detailed information about a specific Adverse Outcome Pathway (AOP) from AOPWiki by AOP ID. Returns the molecular initiating events (MIEs), key events (KEs), adverse outcomes (AOs), stressors (chemicals), and key event relationships (causal chain).

Parameters:

  • aop_id (integer) (required) AOP numeric identifier. Find IDs using AOPWiki_list_aops. Example: 3 (mitochondrial complex I inhibition leading to parkinsonian motor deficits).

Example Usage:

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

AOPWiki_get_key_event (Type: AOPWikiDetailTool)#

Get one AOP-Wiki Key Event (KE) by its numeric event id, including the machine-readable ontology …

AOPWiki_get_key_event tool specification

Tool Information:

  • Name: AOPWiki_get_key_event

  • Type: AOPWikiDetailTool

  • Description: Get one AOP-Wiki Key Event (KE) by its numeric event id, including the machine-readable ontology annotations in its event_components. Each component maps the event to GO / Protein-Ontology / ChEBI terms via process (e.g. ‘aryl hydrocarbon receptor activity’, GO:0004874), object (e.g. ‘aryl hydrocarbon receptor’, PR:000003858), and action (e.g. ‘increased’), plus the biological_organization level (Molecular, Cellular, Tissue, Organ, Individual, Population). Enables cross-database linking and mechanistic toxicology reasoning. Find event ids in the molecular_initiating_events / key_events / adverse_outcomes lists returned by AOPWiki_get_aop. No API key required.

Parameters:

  • event_id (integer) (required) AOP-Wiki Key Event numeric id, e.g. 18 (‘Activation, AhR’). Obtain ids from AOPWiki_get_aop.

Example Usage:

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

AOPWiki_list_aops (Type: AOPWikiListTool)#

List Adverse Outcome Pathways (AOPs) from AOPWiki. Returns AOP IDs, titles, and short names. AOPs…

AOPWiki_list_aops tool specification

Tool Information:

  • Name: AOPWiki_list_aops

  • Type: AOPWikiListTool

  • Description: List Adverse Outcome Pathways (AOPs) from AOPWiki. Returns AOP IDs, titles, and short names. AOPs describe causal chains from molecular initiating events through key events to adverse outcomes, used in toxicology and risk assessment. Pass search to keep only AOPs whose title or short name contains a keyword (e.g. ‘thyroid’, ‘PPAR’, ‘steatosis’) – AOPWiki publishes ~600 AOPs, so an unfiltered list is rarely what you want. Use AOPWiki_get_aop on a returned ID for its key events, stressor chemicals, and causal relationships.

Parameters:

  • search (string) (optional) Case-insensitive keyword to filter AOPs by title or short name. Omit to return every AOP.

Example Usage:

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