Monarch V3 Tools

Configuration File: monarch_v3_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the monarch_v3_tools.json configuration file.

Available Tools

MonarchV3_get_associations (Type: MonarchV3Tool)

Query cross-species associations between biomedical entities in the Monarch Initiative knowledge …

MonarchV3_get_associations tool specification

Tool Information:

  • Name: MonarchV3_get_associations

  • Type: MonarchV3Tool

  • Description: Query cross-species associations between biomedical entities in the Monarch Initiative knowledge graph. Find gene-phenotype, disease-phenotype, gene-disease, or gene-pathway associations. Uses Biolink model categories to specify association type. Integrates data from OMIM, ClinVar, HPO, MGI, ZFIN, FlyBase, WormBase. Example: HGNC:11998 (TP53) with category GeneToPhenotypicFeatureAssociation returns phenotypes like hepatocellular carcinoma and reticular hyperpigmentation.

Parameters:

  • subject (string) (required) Subject entity CURIE. Examples: ‘HGNC:11998’ (TP53), ‘MONDO:0005148’ (type 2 diabetes), ‘HP:0001250’ (seizure).

  • category (string) (required) Biolink association category. Options: ‘biolink:GeneToPhenotypicFeatureAssociation’ (gene->phenotypes), ‘biolink:DiseaseToPhenotypicFeatureAssociation’ (disease->phenotypes), ‘biolink:CorrelatedGeneToDiseaseAssociation’ (gene->diseases, correlated), ‘biolink:CausalGeneToDiseaseAssociation’ (gene->diseases, causal), ‘biolink:GeneToPathwayAssociation’ (gene->pathways), ‘biolink:VariantToDiseaseAssociation’ (variant->diseases).

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

Example Usage:

query = {
    "name": "MonarchV3_get_associations",
    "arguments": {
        "subject": "example_value",
        "category": "example_value"
    }
}
result = tu.run(query)

MonarchV3_get_entity (Type: MonarchV3Tool)

Look up detailed information about any biomedical entity in the Monarch Initiative knowledge grap…

MonarchV3_get_entity tool specification

Tool Information:

  • Name: MonarchV3_get_entity

  • Type: MonarchV3Tool

  • Description: Look up 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 with cross-refs to ENSEMBL, OMIM; MONDO:0005148 returns type 2 diabetes mellitus with detailed description.

Parameters:

  • entity_id (string) (required) Entity CURIE identifier. Examples: ‘HGNC:11998’ (TP53), ‘HGNC:1100’ (BRCA1), ‘MONDO:0005148’ (type 2 diabetes), ‘HP:0001250’ (seizure), ‘OMIM:191170’ (Li-Fraumeni syndrome).

Example Usage:

query = {
    "name": "MonarchV3_get_entity",
    "arguments": {
        "entity_id": "example_value"
    }
}
result = tu.run(query)

MonarchV3_search (Type: MonarchV3Tool)

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

MonarchV3_search tool specification

Tool Information:

  • Name: MonarchV3_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 their CURIE identifiers and categories. Useful for finding entity IDs to use with MonarchV3_get_entity and MonarchV3_get_associations. Example: searching ‘BRCA1’ returns HGNC:1100 (gene), ‘Alzheimer’ returns MONDO disease entries.

Parameters:

  • query (string) (required) Search query. Can be gene names, disease names, phenotype terms, etc. Examples: ‘BRCA1’, ‘breast cancer’, ‘seizure’, ‘insulin resistance’.

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

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

Example Usage:

query = {
    "name": "MonarchV3_search",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)