Monarch Initiative
liveBiologyHealthMonarch biomedical knowledge graph — diseases, phenotypes, genes, variants. Keyless.
Tools
searchrequired: queryFull-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
queryreqstring—categoryoptstring—limitoptnumber—offsetoptnumber—Try it
entityrequired: idSingle node by curie (e.g. "MONDO:0007947").
idreqstring—Try it
associationsrequired: entity_idFetch 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
entity_idreqstring—categoryoptstring—predicateoptstring—directionoptstring—limitoptnumber—Try it
phenotype_to_generequired: phenotype_idGenes annotated to a phenotype (HP:… id).
phenotype_idreqstring—Try it
gene_to_diseaserequired: gene_idDiseases associated with a gene (NCBIGene:… or HGNC:… id).
gene_idreqstring—Try it
Test with curl
The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.
curl -X POST https://gateway.pipeworx.io/monarch-initiative/mcp \
-H "Content-Type: application/json" \
-d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'curl -X POST https://gateway.pipeworx.io/monarch-initiative/mcp \
-H "Content-Type: application/json" \
-d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"search","arguments":{"query": "hello"}}}'Use with the SDK
Install @pipeworx/sdk to call tools from any TypeScript/Node project.
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("search", {"query":"example"});// Or ask in plain English:
const answer = await px.ask("monarch biomedical knowledge graph — diseases, phenotypes, genes, variants");