"How to Query a Knowledge Graph Using an Ontology" matching MCP connectors:

Query STRING interactions, enrichment, annotations, homology, and PPI networks.

QuickGO (EBI) MCP — Gene Ontology browser.

Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants

A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.