The knowledge network

Some knowledge is provided. Some is yours. More connects over time.

Operon reasons over knowledge graphs, not over whatever a model remembers. Each graph stays a separate source with its own identifiers and provenance, and shared identifiers let one question draw on all of them.

By default

MicroMap

A curated, source-linked graph of microbiome biology, hosted by Graphomics and built with MapForge. Every Operon deployment is connected to it.

—Microbes, diseases, compounds, drugs, proteins, pathways and literature
—Every association linked to its sources, with a declared confidence calibration
—Also queryable from your own agents over MCP, or over a REST API

Alongside

Other knowledge graphs

Operon is designed to query additional graphs alongside MicroMap: public reference resources, partner graphs and domain-specific graphs.

—Each graph keeps its own identifiers and provenance
—Federated at the graph layer, not copied into one store
—Added per engagement, as licences allow

Yours

Your Company Graph

Your own graph inside your Operon deployment, built with MapForge from your data and linked to the others by shared identifiers.

—Your datasets, assays, experiments and validated findings
—Grows with every reviewer-approved result
—Private to your organization, never pooled

MicroMap today

Depth you can query, not a static export.

Built from public sources with MapForge, reviewed before anything was written, and extended as new sources are cleared for use.

63,136

source-linked microbe–disease associations, spanning 2,981 microbes and 239 diseases

1.2M+

entities

1.15M+

microbial taxa

2,801

metabolites

2,028

proteins

10,000+

linked papers

60+

API endpoints

Counts as of October 2026.

For your engineers

Query it from the tools you already use.

Access is provisioned per organization. Point Claude Code, Cursor or your own agent at the MCP server, or call the REST API directly. The docs cover both.

Read the Docs

MCP · MicroMap

# find the disease
kg_search(q="colitis")

# which microbes are depleted in it?
kg_disease_taxa(
  disease_id="colitis, ulcerative",
  direction="depleted",
)
# → taxa, each with its studies and PubMed IDs

What it returns

One question, as MicroMap sees it.

Which microbes shift in ulcerative colitis, and what do they produce? Every link below traces to the studies behind it.

Hover or tap a microbe to see its evidence: the studies behind each link, and where the samples came from.

A snapshot of MicroMap (October 2026). Genera with at least two supporting studies; line weight shows the number of studies. Associations are source-linked findings, not causal claims. Common products such as acetate are omitted for legibility.

Hover or tap a microbe to see its evidence: the studies behind each link, and where the samples came from.

A snapshot of MicroMap (October 2026): source-linked findings, not causal claims.

See your own data alongside the reference.

Read the Docs Talk to Us

or emailvkhandavalli@graphomics.com