Monarch New Tools

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

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

Available Tools

Monarch_get_associations (Type: MonarchV3Tool)

Query disease-gene-phenotype associations in the Monarch Initiative knowledge graph. Find gene-ph…

Monarch_get_associations tool specification

Tool Information:

  • Name: Monarch_get_associations

  • Type: MonarchV3Tool

  • Description: Query disease-gene-phenotype associations in the Monarch Initiative knowledge graph. Find gene-phenotype, disease-phenotype, gene-disease, or gene-pathway associations. Provide a subject CURIE (entity of interest) or object CURIE, with optional category filter. Uses the /association/all endpoint. Example: subject=HGNC:11998 returns all TP53 associations including phenotypes and diseases.

Parameters:

  • subject (string) (optional) Subject entity CURIE. Examples: ‘HGNC:11998’ (TP53), ‘MONDO:0005148’ (type 2 diabetes).

  • object (string) (optional) Object entity CURIE. Use instead of subject to find entities associated TO this object.

  • category (string) (optional) Optional Biolink association category filter. Options: ‘biolink:GeneToPhenotypicFeatureAssociation’, ‘biolink:DiseaseToPhenotypicFeatureAssociation’, ‘biolink:CorrelatedGeneToDiseaseAssociation’, ‘biolink:CausalGeneToDiseaseAssociation’, ‘biolink:GeneToPathwayAssociation’.

  • limit (integer) (optional) Maximum associations to return (default: 20, max: 200).

Example Usage:

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

Monarch_get_entity (Type: MonarchV3Tool)

Get detailed information about any biomedical entity in the Monarch Initiative knowledge graph by…

Monarch_get_entity tool specification

Tool Information:

  • Name: Monarch_get_entity

  • Type: MonarchV3Tool

  • Description: Get detailed information about any biomedical entity in the Monarch Initiative knowledge graph by its CURIE identifier. Supports genes (HGNC), diseases (MONDO, OMIM), phenotypes (HP), variants, and more. Returns the entity name, category, description, synonyms, cross-references, and species. Example: HGNC:11998 returns TP53 gene; MONDO:0007739 returns Huntington disease with cross-refs to OMIM, DOID, ICD10.

Parameters:

  • id (string) (required) Entity CURIE identifier. Examples: ‘HGNC:11998’ (TP53), ‘MONDO:0007739’ (Huntington disease), ‘MONDO:0005148’ (type 2 diabetes), ‘HP:0001250’ (seizure).

Example Usage:

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

Monarch_search (Type: MonarchV3Tool)

Search the Monarch Initiative knowledge graph for biomedical entities by name or keyword. Returns…

Monarch_search tool specification

Tool Information:

  • Name: Monarch_search

  • Type: MonarchV3Tool

  • Description: Search the Monarch Initiative knowledge graph for biomedical entities by name or keyword. Returns genes, diseases, phenotypes, and other entities matching the query, with CURIE identifiers and categories. Filter by category (biolink:Gene, biolink:Disease, biolink:PhenotypicFeature) to narrow results. Use returned CURIEs with Monarch_get_entity and Monarch_get_associations for detailed lookups.

Parameters:

  • query (string) (required) Search query: gene names, disease names, phenotype terms. Examples: ‘BRCA1’, ‘Alzheimer’, ‘seizure’, ‘insulin resistance’.

  • category (string) (optional) Filter by entity category. Options: ‘biolink:Gene’, ‘biolink:Disease’, ‘biolink:PhenotypicFeature’. Default: all categories.

  • limit (integer) (optional) Maximum results (default: 10, max: 50).

Example Usage:

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