Ncats Translator Tools#

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

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

Available Tools#

NCATSTranslator_query_associations (Type: NCATSTranslatorTool)#

One-hop biolink association query across ~15 NCATS Translator knowledge providers via the Aragorn…

NCATSTranslator_query_associations tool specification

Tool Information:

  • Name: NCATSTranslator_query_associations

  • Type: NCATSTranslatorTool

  • Description: One-hop biolink association query across ~15 NCATS Translator knowledge providers via the Aragorn reasoner. Given a known entity (entity_id) and a target category and predicate, returns connected entities ranked by score with the primary knowledge source and publication count behind each. Example: entity_id=’MONDO:0004975’ (Alzheimer disease), target_category=’ChemicalEntity’, predicate=’treats’ finds chemicals that treat it. Set target_role=’object’ to instead find entities the known one acts as subject upon.

Parameters:

  • entity_id (string) (required) Translator-normalized CURIE of the known entity, e.g. ‘MONDO:0004975’. Use NCATSTranslator_resolve_entity to find it from a name.

  • target_category (string) (required) Biolink category to search for, e.g. ‘ChemicalEntity’, ‘Gene’, ‘Disease’, ‘PhenotypicFeature’.

  • predicate (string) (required) Biolink predicate linking the two, e.g. ‘treats’, ‘gene_associated_with_condition’, ‘has_phenotype’, ‘causes’.

  • target_role ([‘string’, ‘null’]) (optional) Whether the target (unknown) entity is the predicate’s subject or object: ‘subject’ or ‘object’. entity_id takes the other role. Default ‘subject’ (e.g. ‘chemical treats disease’ with entity_id as the disease).

  • limit ([‘integer’, ‘null’]) (optional) Max results to return, 1-100. Default 25.

Example Usage:

query = {
    "name": "NCATSTranslator_query_associations",
    "arguments": {
        "entity_id": "example_value",
        "target_category": "example_value",
        "predicate": "example_value"
    }
}
result = tu.run(query)

NCATSTranslator_resolve_entity (Type: NCATSTranslatorTool)#

Resolve a free-text biomedical name to Translator-normalized identifiers (CURIEs) via SRI Name Re…

NCATSTranslator_resolve_entity tool specification

Tool Information:

  • Name: NCATSTranslator_resolve_entity

  • Type: NCATSTranslatorTool

  • Description: Resolve a free-text biomedical name to Translator-normalized identifiers (CURIEs) via SRI Name Resolution. Returns matches ranked by relevance with their biolink categories, species, and a synonym sample. Example: name=’Alzheimer disease’ returns curie=’MONDO:0004975’. Use the returned curie as entity_id in NCATSTranslator_query_associations.

Parameters:

  • name (string) (required) Free-text name, e.g. ‘Alzheimer disease’, ‘aspirin’, ‘BRCA1’.

  • limit ([‘integer’, ‘null’]) (optional) Max matches to return, 1-20. Default 10.

  • biolink_type ([‘string’, ‘null’]) (optional) Optional biolink category filter, e.g. ‘Disease’, ‘ChemicalEntity’, ‘Gene’.

Example Usage:

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