is a Knowledge Graph.
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).
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Github: vkhangraphomics
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| micromap.api | MicroMap API | docs | Programming Interface | http | REST API and MCP server over the prod... |
| micromap.mapforge | MicroMap MapForge | micromap-mapforge | Process | python | MapForge, the reviewable ingestion pi... |
| micromap.schema | MicroMap Neo4j Schema | neo4j_microbiome_schema.cypher (4.3 KB) | Data Model | neo4j | Neo4j graph schema for MicroMap, defi... |
MicroMap is a microbiome knowledge graph platform from Graphomics. It runs on Neo4j and connects microbial taxa to diseases, metabolites, pathways, drugs, genes, proteins, body sites and papers.
The loader in the open-source repository has entry points for NCBI Taxonomy, Disbiome, gutMDisorder, BugSigDB, GMrepo, mBodyMap, HMDB, KEGG, ChEMBL, Reactome, PubChem, PubMed and SemMedDB, plus curated taxon-metabolite production and gut-brain axis association tables. Release v0.1.3 removed the loaders for three third-party sources whose commercial licensing terms were under review at the time. The source list above reflects the v0.1.4 code.
Node labels: Taxon, Disease, Compound, Pathway, Gene, Drug,
Protein, Paper, Study, BodySite, DrugClass. Relationship types
include ASSOCIATED_WITH_DISEASE, PRODUCES, PARTICIPATES_IN, TARGETS,
FOUND_IN, HAS_PARENT and IMPLICATED_IN.
Data enters the graph through MapForge. MapForge inspects a tabular source, drafts a mapping, resolves source entities against the graph, emits a parameterized Cypher bundle and submits it to Neo4j only after a reviewer approves the bundle. Every submission records who contributed, who approved, source-file hashes and resolved and unresolved counts.
The ingestion software, API code and graph schema are public at
https://github.com/vkhangraphomics/micromap-oss. The populated production
graph is served to Graphomics customers through a REST API (API key in the
X-API-Key header) and an MCP server. It is not distributed as a bulk
download. The code can be run against a local Neo4j instance to build a
graph from the supported sources.
The MIT license covers the ingestion software, the API code and the graph schema. It does not cover the populated graph or the upstream data, which carry their own terms.
An unrelated resource named MicroMap, a microbiome-metabolism network visualization tool from the Thiele lab at the University of Galway, was published in npj Biofilms and Microbiomes in 2025 and is hosted on Harvard Dataverse. The two projects share a name and a field and nothing else.
Created: September 16, 2026 | Last modified: September 23, 2026