Ontology Atlas MCP Server

Ontology Atlas

<p align="center"> <picture> <source media="(prefers-color-scheme: dark)" srcset="public/brand/lockup-dark@2x.png" /> <img src="public/brand/lockup-light@2x.png" alt="Ontology Atlas — Understand your codebase." width="360" /> </picture> </p> <p align="center"> <strong>Understand your system as AI agents change its code.</strong><br /> _{Give agents task context. Inspect the meaning, evidence, and unknowns yourself.} </p> <p align="center"> <a href="https://ontologyatlas.com/en/download/"><strong>Download for macOS</strong></a> · <a href="https://ontologyatlas.com/en/download/"><strong>Windows x64 beta</strong> _unsigned</a> · <a href="https://ontologyatlas.com/en/topology/">Live demo</a> · <a href="https://ontologyatlas.com/en/guide/">Guide</a> · <a href="#status--read-this-before-installing">Status</a> </p> <p align="center"> <a href="LICENSE"><img alt="MIT license" src="https://img.shields.io/badge/license-MIT-5e6ad2.svg" /></a> <a href="mcp/README.md"><img alt="MCP runtime inventory" src="https://img.shields.io/badge/MCP-runtime_inventory-5e6ad2.svg" /></a> <a href="cli/README.md"><img alt="Local CLI" src="https://img.shields.io/badge/CLI-local_tools-5e6ad2.svg" /></a> <img alt="Local-first" src="https://img.shields.io/badge/storage-local--first-17181f.svg" /> <a href="https://mcpservers.org/servers/wlsdks/ontology-atlas"><img src="https://mcpservers.org/badge.svg" alt="Listed on mcpservers.org" height="20" /></a> </p>

<p align="center">_{Every screenshot reads <a href="samples/storefront"><code>samples/storefront</code></a>, an online store described by Markdown files in this repository.}</p>

In 30 seconds

What	An atlas/ folder of Markdown inside your repository. Each file's frontmatter says what it is (project, domain, capability, element, document) and what it points at. That folder is the whole database.
For your agent	Typed task context over MCP: capabilities, code anchors, declared dependencies, evidence, and unknowns.
For you	The same records on a map, in documents, and as Git diffs, so you decide which meaning changes to keep.
Honest by design	A graph path is a declared relationship, not proof of runtime impact. Missing evidence shows as unknown, never as safe.

your-repo/
├── src/
└── atlas/                 ← the whole ontology, cloned, branched and reviewed with the code
    ├── project.md
    ├── domains/  capabilities/  elements/
    ├── sources/           documents kept exactly as they arrived
    └── wiki/              pages written from those sources, every fact cited

See it

<table> <tr> <td width="50%"><img src="docs/assets/readme/topology-focus.png" alt="The map with the Orders domain selected: unrelated concepts recede, the concepts it contains are named, and the inspector lists contains, used by, leans on and belongs to" /><br /><b>Map</b> — select a concept; everything unrelated recedes.</td> <td width="50%"><img src="docs/assets/readme/three-dimensional-views.png" alt="The map picker offering Flat, Galaxy, Cone, Strata and Neural views" /><br /><b>Five views</b> — Flat, Galaxy, Cone, Strata and Neural.</td> </tr> <tr> <td><img src="docs/assets/readme/agent-connect.png" alt="The Agents screen listing the coding tools found on this computer with their readiness and a chat or connection check for each" /><br /><b>Agents</b> — chat with Claude Code or Codex inside the app.</td> <td><img src="docs/assets/readme/mcp-connect.png" alt="The MCP screen with one connect button each for Claude Code, Codex, Cursor and Antigravity" /><br /><b>MCP</b> — one button per agent, then a live connection proof.</td> </tr> <tr> <td><img src="docs/assets/readme/library-sources.png" alt="The Library with gathered sources, their format and size, and the Gather, Compile and Read stages" /><br /><b>Library</b> — gather any document, compile cited wiki pages.</td> <td><img src="docs/assets/readme/docs-workspace.png" alt="The Library Ontology workspace with the vault tree, a capability document, its frontmatter and backlinks" /><br /><b>Documents</b> — edit the Markdown that becomes the graph.</td> </tr> <tr> <td><img src="docs/assets/readme/architecture-flow.png" alt="The Architecture screen comparing reviewed roles against the imports observed in code" /><br /><b>Architecture</b> — reviewed roles against the imports in code.</td> <td><img src="docs/assets/readme/relation-review.png" alt="A relation review beside the map showing the before and after lists and the reason that will be written" /><br /><b>Relation review</b> — see before and after, then confirm.</td> </tr> <tr> <td><img src="docs/assets/readme/history-review.png" alt="The History screen with an unsaved concept change, its exact Markdown diff, and Fetch, Pull and Push" /><br /><b>History</b> — the exact Markdown diff before you save.</td> <td><img src="docs/assets/readme/graph-insights.png" alt="The Analysis screen with measurements above tabs and the things to fix grouped by kind" /><br /><b>Analysis</b> — what to fix next, by measurement, not a score.</td> </tr> </table>

How it works

1. Open a folder — the app reads Markdown in place, or starts atlas/ from your code. The path is shown before anything is written.
2. Connect your agent — one button writes the MCP config; a restart and mcp-verify prove the connection is live.
3. Ask for context — query_ontology with operation: "agent_brief" gives the agent a bounded brief for its task.
4. Review the meaning — proposed changes arrive as Markdown diffs; you keep, correct, or reject them in Git.

Definition previews preserve complete introductory text; the full document retains exclusions and uncertainties. Local code inspections show the connected folder and offer native permission recovery before reading.

$ node $ATLAS blast-radius capabilities/mcp-tool-server docs/ontology --depth 2
capabilities/mcp-tool-server — blast radius (depth 2, incoming)
  risk unknown · 1 node · 1 relation · 0 cross-domain

<details> <summary><b>What one node looks like</b></summary>

---
uid: 71890f3e-7b5d-4c0a-8f14-123456789abc   # permanent identity, kept through renames
slug: capabilities/token-issue
kind: capability
title: Token issue
domain: domains/auth
path: src/auth/token-service.ts          # a path — code evidence
elements:
  - elements/jwt-signer                  # a slug — an implementation-role node
dependencies:
  - capabilities/session-refresh         # a slug — another node
---

Issues access and refresh tokens for authenticated users.

A path points at code; a slug points at a node. dependencies are directed and relates is symmetric, so the map never turns similarity into causality. Only files with kind: join the graph; sources/** and wiki/** pages do not. Full contracts: what becomes a node? · relations · vault specification.

</details>

Principles

Local-first	Not a…
Your disk is the database; Git is the history.	general-purpose ontology editor
No Atlas backend, account, or telemetry.	code index or IDE
Model and provider transfers are opt-in and logged in .ontology-atlas/llm-audit.jsonl.	automatic acceptance of generated knowledge
MCP and CLI read the folder directly, even with the app closed.	RDF/OWL/SHACL implementation (§5.2)
Extensions are files a git diff shows you, never third-party code.	service, and not on npm

Measured, honestly: our first benchmark mostly tested vocabulary only Atlas knew. Re-scored, we have not yet measured a difference in answer quality, and Atlas was slower. The correction · benchmark log.

Status — read this before installing

• The download page is the release authority: tag, sizes, checksums, and signing state. GitHub Releases is the second source.
• macOS is Developer ID signed and notarized, with the MCP server inside the bundle.
• Windows x64 is an unsigned beta — SmartScreen may warn, and a managed PC may refuse it. See Security.
• Linux and others run the browser app, or the CLI and MCP server from a source checkout.
• Every release is a plain version; the in-app updater verifies each archive's signature before installing.

Documentation

Use it: hosted guide · features · MCP setup · CLI reference<br /> Model a vault: what becomes a node? · relations · specification · quality authority map<br /> Understand it: product direction · architecture · security · decisions

Contributing

Issues and pull requests are welcome; the most useful report points Atlas at a real repository and shows where it falls short. Read CONTRIBUTING.md first (external pull requests come from forks), and AGENTS.md is canonical for people and agents alike. Start with pnpm checks:changed -- --run; land with pnpm pr:land <number>.

<details> <summary><b>Repository commands</b></summary>

Command	What it answers
pnpm agents:check	Each harness's instruction integrity; independent Codex and Claude files need not match
pnpm backlog · pnpm backlog:check	Current task records and concurrent-state conflicts; append a UUID record per worktree observation (guide)
pnpm bundle:plan · pnpm bundle:prune	Land several branches as one: plan the merge (which carry work, shared files, trial conflicts) and afterwards prune the component branches main provably contains. See /land-bundle
pnpm checks:changed	Which gates this change actually needs
pnpm conflicts:scan	Which open pull requests (and -- --match=<glob> local branches) change the same files as this branch, and whether a trial merge with each conflicts; read-only, one gh call
pnpm decisions:find <terms> · pnpm decisions:check	The decision record to cite or overturn, and whether this change owes one
pnpm doc:new -- --type=<kind> --area=<area> --slug=<slug>	A new living document from its template in docs/.templates/, at the path its kind decides
pnpm docs:check	Docs gates, including pnpm docs:language, pnpm source:language, pnpm changelog:check, pnpm dev-checks:check, pnpm docs:meta
pnpm docs:meta · pnpm doc:history -- <path>	Whether every living document carries its kind, status and area with pointers that resolve; one document's commits across moves, which is its version
pnpm docs:move	Moves the documents listed in docs/.moved.json and rewrites every reference; rerun it after merging main into an older branch (-- --check only reports)
pnpm e2e:durations -- <timings dir>	Rewrites the per-file weights that balance the browser shards from downloaded playwright-timings-* reports
pnpm e2e:sleeps:check	A change may not add a fixed waitForTimeout to an e2e spec unless a // measurement window: note says why
pnpm gates:yield -- --runs=200	Which CI checks ever failed, per distinct run, from the lane reports checks.yml uploads (cached in ~/.cache/atlas-gate-yield); a row with 50+ runs, no failed run and 60+ days of history reads no CI failure, a check to examine rather than delete, since pre-push and pnpm checks:changed catches are not in this data. Reports start with the change that added them
pnpm gateway:capture -- --base-url=<static export>	Re-shoots the six app screens the download page shows, Korean and English (public/gateway/<screen>.<locale>.png), from a served pnpm build, against this repository's own ontology
pnpm knip	Dead files, exports and types across every scope
pnpm lessons · pnpm lessons:check	Shared harness lessons that are open or verified but not yet fixed; record and review them with /harness-retro (records guide)
pnpm messages:build · pnpm messages:check · pnpm messages:adopt	Compose the ignored messages/<locale>.json from one file per namespace (messages/<locale>/<Namespace>.json), prove it current, and carry a pre-split branch's catalogue edits onto the parts while merging main
pnpm perf:mcp:memory · pnpm perf:mcp:memory:check	Whether the MCP server keeps memory it should release: heap after two forced collections across 50 repeated calls per tool and across moved Git HEADs, on a generated vault; about a minute, kept out of pre-push
pnpm pr:ci <n>	Fire CI on a draft now, so a green, disjoint change can take the fast path
pnpm pr:land --plan <n...> · pnpm pr:land --conduct	Dry-run what a landing would do without writing to GitHub, and run trains until the queue is empty
pnpm pr:land <n> · pnpm pr:queue	Queue a pull request for the landing train (or merge it on the fast path), and show the queue and the train in flight
pnpm typecheck	Types across every file, with Next's generated route and page types, so the browser build need not check them again

Rows stay sorted by command, and the reference's entries by area, so two branches that each add one land on different lines; pnpm dev-checks:check names the line to move and -- --fix sorts both. Development checks is the full gate reference, one entry per area; map testability owns canvas performance, readability, contrast, and instrumentation.

</details>

License

MIT