@pipeworx/monarch-initiative

Connect: https://pipeworx.io/mcp — every tool in the catalog, including @pipeworx/monarch-initiative’s. Install: one-click buttons

No MCP client? Skip the connection: POST https://gateway.pipeworx.io/v1/tools/search_packs {"query":"..."} to find a tool below, GET /v1/tools/<name> for its schema, POST the same URL with arguments for the data — see For AI agents.

Tools: 5

Monarch Initiative MCP — biomedical knowledge graph linking diseases, phenotypes, genes, and variants across species. Keyless.

Tools

• search(query, category?, limit?, offset?) — full-text node search
• entity(id) — single node by curie (e.g. MONDO:0007947)
• associations(entity_id, category?, predicate?, direction?, limit?) — associations involving an entity
• phenotype_to_gene(phenotype_id) — gene candidates for a phenotype (HP:…)
• gene_to_disease(gene_id) — diseases associated with a gene

Data source

https://api.monarchinitiative.org/v3/api/

Tools

• search — Full-text search across the Monarch biomedical knowledge graph for diseases, genes, phenotypes, and other biolink entities by query string; filter by category (e.g. biolink:Disease) and paginate with
• entity — Single node by curie (e.g. “MONDO:0007947”).
• associations — Fetch biolink associations (edges) involving a Monarch entity by its CURIE ID (e.g. MONDO:0007947); filter by association category (e.g. biolink:DiseaseToPhenotypicFeatureAssociation), predicate, or d
• phenotype_to_gene — Genes annotated to a phenotype (HP:… id).
• gene_to_disease — Diseases associated with a gene (NCBIGene:… or HGNC:… id).