mykg

myKG — The Knowledge Graph Engine

myKG automatically generates a confidence-scored knowledge graph from a set of mixed documents — Markdown, plain text, PDF, Word, PowerPoint, Excel, HTML, and images — grounded in an induced RDFS/OWL ontology.

Updates

• v0.4.10 — Schema drift detection and pruning: mykg detect-schema-drift reports concepts and properties the graph no longer uses, and mykg prune-schema removes them (with --preview, an editable plan file, and a backup). See Schema Drift & Pruning.

• v0.4.9 — The nodes.jsonl, edges.jsonl and knowledge_graph.ttl exports now stream to disk record by record instead of building the whole file in memory first, so peak memory stays flat as the graph grows.

• v0.4.8 — mykg_search_nodes and mykg_query_graph's seed selection now use BM25 instead of a linear substring scan, ~2,800x faster at 100K nodes (0.5ms vs. 1.4s per query) and no longer degrading to minutes per query as the graph grows.

Contents

• Features
• Quick Start
• Command line
• Articles & Tutorials
• Configuration
• Extract Pipeline
  • Running
  • Sessions
  • Pipeline Steps
• Outputs
• MCP (Model Context Protocol) Server
• Using mykg with Claude Code
  • Agent mode (Claude Code skill)
  • claude-cli profile
• Advanced Options
  • Re-running from a Specific Step
  • Orphan-Connection Pass
  • Human Review Gate
  • Locked Base Schema
  • SKOS Thesaurus
  • Website / Repo Fetching
  • Standalone Document Conversion
  • Append Mode
    • Incremental Schema Growth
  • Merging Sessions
  • Walkthrough Report
  • Schema Drift & Pruning
  • Obsidian Vault Export
  • Neo4j Load CSV Export
• Troubleshooting
• Roadmap
• Development
  • Testing
  • Healthiness check
• Design
• License

Features

MyKG builds trustworthy knowledge graphs through a self-evolving ontology that continuously adapts, maintains consistency, and assigns confidence scores to knowledge, keeping information grounded and reliable as it grows.

Ontology-Guided Extraction

• Schema-guided knowledge graph generation — the extracted graph is always grounded in a formal RDFS/OWL schema: concept types, property names, domain/range constraints, and the is-a hierarchy are explicit and inspectable before any entity is extracted

• AI coding assistant friendly — designed for smooth use alongside AI coding assistants such as Claude Code; Use the Claude Code Skill to run extractions, inspect outputs, and iterate on your knowledge graph without leaving your coding environment; see Using mykg with Claude Code

• Second brain for AI coding assistants — the Obsidian vault output turns your extracted knowledge graph into a directory of wikilinked Markdown notes that any AI coding assistant can read as project context; point Claude Code, Cursor, or Copilot at output/obsidian_vault/ and ask questions, trace relationships, and get answers grounded in your own documents

• MCP server for desktop AI apps — run mykg mcp-serve to expose your knowledge graph via the Model Context Protocol; integrates with Claude Desktop, Cherry Studio, and any MCP-compatible client — 16 query tools let LLMs search entities, explore relationships, find paths, traverse the graph, and read wiki notes directly from your extracted knowledge; see MCP Server

• Incremental updates — append new files to an existing session, extracting only what changed. Optionally grow the schema from new documents while preserving existing concepts and properties

• Resumable pipeline — every stage persists intermediate state; re-enter at any step after a crash or edit

• Session isolation — each run is fully self-contained; inputs, intermediate state, outputs, and logs co-located

• Cross-session merge — combine two independently-produced graphs into one unified knowledge graph

• Bring your own ontology — supply a --base-schema TTL file (RDFS or OWL) to lock in classes and properties from an existing formal ontology; the LLM expands it with domain-specific concepts but will not rename, remove, or contradict your authoritative vocabulary. Please note that this mechanism is controlled by the LLM, and may not be strictly enforced. Add --freeze-schema to skip LLM schema induction entirely and extract from the documents strictly against your ontology verbatim — no surprise types, no invented properties

• SKOS thesaurus support — pass --thesaurus to load a SKOS vocabulary; skos:exactMatch terms are collapsed silently, skos:closeMatch terms trigger a warning — giving the schema merger richer synonym awareness than string matching alone

• Verifiable TTL ontology — after Pass 1, the induced schema is exported as a valid RDFS/OWL Turtle file (intermediate/schema.ttl) that can be opened directly in ontology editors such as Protégé. The TTL is validated by rdflib (syntax + semantic checks: domain/range refer to declared classes, no conflicting ranges) before any extraction begins

• Human-in-the-loop ontology design — pause after schema induction with --review, edit the schema, and resume extraction. Edit schema.json directly or refine schema.ttl in Protégé and feed it back with --freeze-schema

Input

• Mixed-format corpora — point mykg extract-graph at any directory; supported extensions are converted to Markdown automatically before ingest:

  Format	Extensions	Backend
  Markdown	.md	passthrough (consumed as-is)
  Plain text	.txt	renamed to .md in-process
  PDF, Word, PowerPoint, Excel, images	.pdf .docx .doc .pptx .xlsx .png .jpg .jpeg	MinerU in an ephemeral uv-managed Python 3.12 venv — nothing is installed into your active environment
  HTML	.html .htm	markdownify in-process; anchors and image tags stripped
  Websites, GitHub repos	any URL	Crawlee in an ephemeral uv venv — produces an mykg_web_fetch/ folder

  Anything outside the allowlist (e.g. .svg, .css, .php assets next to an HTML bundle) is logged and skipped, never silently dropped. The allowlist is configurable via preprocess.extensions in mykg_config.yaml.

  Incremental conversion — unchanged source files are skipped on re-run. Adding one PDF to a corpus and re-running only re-converts that PDF. Force a full re-conversion with mykg extract-graph --from-step preprocess.

Graph & Output

• Provider-agnostic — works with Anthropic (Claude), OpenAI (GPT), Google Gemini, Ollama (local), OpenRouter, or the claude CLI
• Five output families — JSONL for Neo4j/NetworkX/RAG, Turtle RDF for OWL toolchains, NetworkX multi-format for graph analysis, Obsidian vault for linked personal knowledge management, and an optional Neo4j LOAD CSV bundle (plain-header CSVs + paste-and-run Cypher script for Neo4j Browser / cypher-shell)
• Obsidian vault — second brain for AI coding assistants — every extracted entity becomes a wikilinked Markdown note in output/obsidian_vault/; open it in Obsidian to navigate the graph with backlinks and Graph View, or point your AI coding assistant (Claude Code, Cursor, Copilot) at the vault folder so it can answer questions, trace relationships, and reason over your knowledge base in natural language
• Interactive HTML graph — node/edge filtering, search, hover popups; opens directly in a browser
• Confidence scoring — every extracted attribute, node, and edge carries a 0.0–1.0 confidence score

Quick Start

Requires Python 3.11+ (developed on macOS; automated CI runs the test suite on Ubuntu and Windows), and one of: an Anthropic/OpenAI/Gemini/OpenRouter API key, Ollama running locally, or the claude CLI.

Install from PyPI

Install mykg, then run the interactive setup wizard — it asks for your provider, model, and API key and writes mykg_config.yaml and .env.mykg in one step.

pip install mykg
mykg init

Then extract a knowledge graph from your notes:

mykg extract-graph my_notes/

Open mykg_sessions/<timestamp>/output/knowledge_graph.html in your browser to explore the result.

Install from source

Install uv, clone the repo, sync dependencies, run the setup wizard, then extract.

git clone https://github.com/SenolIsci/mykg && cd mykg
uv sync && uv run mykg init --force

Then extract a knowledge graph from your notes:

uv run mykg extract-graph my_notes/

For Ollama (local inference, no API key needed), pull a model and select the ollama-local profile when mykg init prompts you.

ollama pull llama3.3
mykg init
mykg extract-graph my_notes/

Command line

All Commands