npm package: @ontomics/ontomics
Description: MCP server that extracts domain ontologies from Python codebases
Latest version: 0.3.0

# ontomics

![Python](https://img.shields.io/badge/Python-3776AB?logo=python&logoColor=white)
![Rust](https://img.shields.io/badge/Rust-000000?logo=rust&logoColor=white)
![TypeScript](https://img.shields.io/badge/TypeScript-3178C6?logo=typescript&logoColor=white)
![JavaScript](https://img.shields.io/badge/JavaScript-F7DF1E?logo=javascript&logoColor=black)
![platform](https://img.shields.io/badge/macOS_·_Linux-grey)
![MCP](https://img.shields.io/badge/MCP_Server-green)
[![MCP Registry](https://img.shields.io/badge/MCP_Registry-listed-blue)](https://registry.modelcontextprotocol.io/)
![Claude Code](https://img.shields.io/badge/Claude_Code-cc785c?logo=anthropic&logoColor=white)
![Codex](https://img.shields.io/badge/Codex-black?logo=openai&logoColor=white)
![pi](https://img.shields.io/badge/pi--coding--agent-blue)

ontomics extracts domain knowledge from codebases to reduce LLM token consumption by 20x and time in agentic search by 10x. It gathers the concepts, naming conventions, and vocabulary embedded in your code and makes them queryable via [MCP](https://modelcontextprotocol.io/).

## Benchmark

Tested with Claude Sonnet — same question, with and without ontomics.

"What does 'transform' mean in this codebase?" on [voxelmorph](https://github.com/voxelmorph/voxelmorph) ([full transcript](doc/benchmarks/transform-voxelmorph.md)):

|                | With ontomics | Without    |
|----------------|---------------|------------|
| Tool calls     | 1             | 19         |
| Tokens         | ~3.7k         | ~76k       |
| Time           | 5s            | 1m 15s     |
| Answer quality | Complete      | Complete   |

"What are the main domain concepts in this codebase?" on [ScribblePrompt](https://github.com/halleewong/ScribblePrompt) ([full transcript](doc/benchmarks/concepts-scribbleprompt.md)):

|                | With ontomics | Without    |
|----------------|---------------|------------|
| Tool calls     | 1             | 26         |
| Tokens         | ~3.7k         | ~61.6k     |
| Time           | ~5s           | 56s        |
| Answer quality | Complete      | Complete   |

Both conditions produced complete, correct answers. ontomics got there in one call.

## What it does that search can't

Search tells you where a string appears. An LSP tells you where a symbol is defined and referenced. Neither answers: what are the domain concepts in this codebase? How do they relate? What naming conventions emerged? What changed in the domain vocabulary since last release?

ontomics builds a semantic index of your project's domain — clustering related symbols into concepts, detecting naming conventions from usage frequency, resolving abbreviations, and tracking how the vocabulary evolves over time. That index can be exported as a portable artifact to bootstrap conventions in other repos.

## Install

Install once, available in every project. No configuration needed — ontomics auto-detects the repo and indexes it on first run.

ontomics requires a git repository (`.git/` directory). It will refuse to index home, root, or temp directories. To index a non-git directory, pass `--force`.

### 1. Install the binary

**npm (macOS/Linux):**
```bash
npm install -g @ontomics/ontomics
```

**macOS (Homebrew):**
```bash
brew install EtienneChollet/tap/ontomics
```

**Shell installer (macOS/Linux):**
```bash
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/EtienneChollet/ontomics/releases/latest/download/ontomics-installer.sh | sh
```

**From source:**
```bash
git clone https://github.com/EtienneChollet/ontomics.git
cd ontomics
cargo build --release
```

### 2. Register with your harness

**Claude Code:**
```bash
claude mcp add -s user ontomics -- ontomics
```

**Codex:**
```bash
codex mcp add ontomics -- ontomics
```

**OpenClaw:**
```bash
openclaw mcp set ontomics '{"command":"ontomics"}'
```

**pi-coding-agent:**
```bash
pi install npm:@ontomics/ontomics
```

**Share with your team** — drop an `.mcp.json` in your repo root:
```json
{
  "mcpServers": {
    "ontomics": {
      "command": "npx",
      "args": ["-y", "@ontomics/ontomics", "--repo", "."]
    }
  }
}
```

## Supported languages

Python, TypeScript, JavaScript, Rust. Auto-detected from file extensions.

## Tools

| Tool | What it does |
|------|--------------|
| `query_concept` | Find all variants, related concepts, and occurrences of a term |
| `locate_concept` | Find the key signatures, classes, and files for a concept |
| `describe_symbol` | Get the signature, docstring, and relationships for a function or class |
| `trace_concept` | Trace how a concept flows through the codebase via call chains |
| `list_concepts` | List the top domain concepts by frequency |
| `list_conventions` | List all detected naming patterns (prefixes, suffixes, conversions) |
| `list_entities` | List code entities (classes, functions) filtered by concept, role, or kind |
| `check_naming` | Check an identifier against project conventions; suggests the canonical form |
| `suggest_name` | Generate an identifier name that fits the project's vocabulary |
| `vocabulary_health` | Measure convention coverage, naming consistency, and cluster cohesion |
| `ontology_diff` | Show new, changed, or removed domain concepts since a git ref |
| `export_domain_pack` | Export domain knowledge as portable YAML for use in other repos |

### Resources

| Resource | What it does |
|----------|--------------|
| `ontomics://briefing` | Session briefing: top conventions, abbreviations, key concepts, contrastive pairs, and vocabulary warnings. Also available via `ontomics briefing` CLI. |

## How it works

ontomics parses every file in your repo, extracts identifiers and docstrings, clusters related terms by embedding similarity, and detects naming conventions through frequency analysis. The index lives at `<repo>/.ontomics/index.db` — subsequent startups load from cache and watch for changes.

Configuration via `.ontomics/config.toml` in the repo root. All fields have sensible defaults. See `SPEC.md` for the full design contract.