MicroMap is a microbiome knowledge graph platform built by Graphomics on Neo4j. It links microbial taxa to diseases, metabolites, pathways, drugs, genes, proteins, body sites and literature. The graph is populated through MapForge, a BioCypher-compatible ingestion pipeline that turns tabular source data into parameterized Cypher bundles that a reviewer approves before any node is written. Loaders cover NCBI Taxonomy, Disbiome, gutMDisorder, BugSigDB, GMrepo, mBodyMap, HMDB, KEGG, ChEMBL, Reactome, PubChem, PubMed and SemMedDB. The ingestion software, API code and graph schema are open source under the MIT license. The populated production graph is served to Graphomics customers through a REST API and an MCP server and is not distributed as a bulk download. This resource is unrelated to the MicroMap microbiome-metabolism visualization resource from the Thiele lab (University of Galway, 2025).
Graph at a glance
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