Oncotree Tools#

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

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

Available Tools#

OncoTree_get_type (Type: OncoTreeGetTypeTool)#

Get complete information about one OncoTree cancer type by exact code (e.g. ‘BRCA’, ‘LUAD’, ‘GBM’…

OncoTree_get_type tool specification

Tool Information:

  • Name: OncoTree_get_type

  • Type: OncoTreeGetTypeTool

  • Description: Get complete information about one OncoTree cancer type by exact code (e.g. ‘BRCA’, ‘LUAD’, ‘GBM’). The wrapper requires one unique upstream result and verifies its code before success. Returns name, main type, tissue, hierarchy, color, history, children, precursors, revocations, and UMLS/NCI references. A missing code returns an explicit not-found error rather than a generic HTTP error.

Parameters:

  • code (string) (required) OncoTree cancer type code (case-insensitive). Examples: ‘BRCA’ (Invasive Breast Carcinoma), ‘LUAD’ (Lung Adenocarcinoma), ‘GBM’ (Glioblastoma Multiforme), ‘PAAD’ (Pancreatic Adenocarcinoma).

  • version (string) (optional) OncoTree version. Default: ‘oncotree_latest_stable’.

Example Usage:

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

OncoTree_list_tissues (Type: OncoTreeListTissuesTool)#

List all tissue categories in the OncoTree hierarchy. Returns the unique set of tissue/organ name…

OncoTree_list_tissues tool specification

Tool Information:

  • Name: OncoTree_list_tissues

  • Type: OncoTreeListTissuesTool

  • Description: List all tissue categories in the OncoTree hierarchy. Returns the unique set of tissue/organ names used as top-level groupings (e.g. ‘Breast’, ‘Lung’, ‘Brain/CNS’, ‘Bladder/Urinary Tract’). Use to discover what tissues are represented in OncoTree before searching by tissue, or to enumerate all supported cancer tissue origins.

Parameters:

  • version (string) (optional) OncoTree version. Default: ‘oncotree_latest_stable’.

Example Usage:

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

OncoTree_search (Type: OncoTreeSearchTool)#

Search the OncoTree cancer type ontology by name, code, main type, or tissue. Returns every upstr…

OncoTree_search tool specification

Tool Information:

  • Name: OncoTree_search

  • Type: OncoTreeSearchTool

  • Description: Search the OncoTree cancer type ontology by name, code, main type, or tissue. Returns every upstream field for each matched tumor type, including color, hierarchy children, history, precursors, revocations, and UMLS/NCI references. An upstream HTTP 404 for no matches is normalized to a successful empty result. Exact name/code searches are checked against every returned record; metadata confirms source-record completeness and the requested version.

Parameters:

  • query (string) (required) Search term. Interpreted according to the ‘field’ parameter. Examples: ‘breast cancer’, ‘BRCA’, ‘Lung’, ‘Non-Small Cell Lung Cancer’.

  • field (string) (optional) Field to search in. One of: ‘name’ (cancer type name), ‘code’ (OncoTree code), ‘main_type’ (main cancer category), ‘tissue’ (tissue of origin). Default: ‘name’.

  • exact_match (boolean) (optional) If true, requires exact match. If false (default), performs substring/prefix matching.

  • version (string) (optional) OncoTree version identifier. Use ‘oncotree_latest_stable’ (default) for the current production version.

Example Usage:

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