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 Monarch with exact offset pagination. Provide a subj…

Monarch_get_associations tool specification

Tool Information:

  • Name: Monarch_get_associations

  • Type: MonarchV3Tool

  • Description: Query disease-gene-phenotype associations in Monarch with exact offset pagination. Provide a subject or object CURIE; metadata reports total_results, has_more and next_offset.

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) Associations per page (1-200).

  • offset (integer) (optional) Zero-based offset. Continue with metadata.next_offset.

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 knowledge graph for biomedical entities with exact offset pagination. Metadata…

Monarch_search tool specification

Tool Information:

  • Name: Monarch_search

  • Type: MonarchV3Tool

  • Description: Search the Monarch knowledge graph for biomedical entities with exact offset pagination. Metadata reports total_results, has_more and next_offset.

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) Results per page (1-50).

  • offset (integer) (optional) Zero-based offset. Continue with metadata.next_offset.

Example Usage:

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