Simple Graph Builder

This plugin builds a lightweight knowledge graph from users' Obsidian notes using LLM-powered entity extraction with a simple yet expressive ontology model to provide knowledge extraction, exploration, and RAG search. Since Obsidian provides wonderful links between notes, implementing ontology model would meet users' (especially researchers') needs.

Why Lightweight Ontology?

Traditional knowledge graphs often require complex schemas with dozens of entity and relationship types, making them difficult to maintain and query. Simple Graph Builder takes a different approach:

• 10 Fixed Entity Types: PERSON, ORGANIZATION, CONCEPT, PROJECT, TOOL, EVENT, PLACE, DOCUMENT, METHOD, TOPIC - covering all common knowledge domains
• Free-form Relationship Verbs: Express relationships naturally with active verbs like "develops", "uses", "causes", "cites"
• Detail Property: Each relationship includes a detail field for nuanced descriptions without schema explosion

This design provides structured entity classification with expressive relationships, making it easy to build, query, and maintain your personal knowledge graph.

Features

• Lightweight Ontology Model: Simple but expressive - 10 fixed entity types + free-form relationship verbs with detail annotations
• Hybrid Entity Resolution: Multi-stage deduplication pipeline combining fast lookups with embedding similarity and LLM verification (inspired by KGGen [3])
• Smart Search: AI-powered natural language queries over your knowledge graph with multi-path exploration
• Entity Extraction: Automatically extract entities from your notes using AI (configurable extraction depth)
• Schema-enforced Extraction: Every extraction request carries a JSON schema, and replies are validated against it — malformed entities are reported and dropped rather than silently polluting the graph
• Internal Link Support: Automatically processes [[wikilinks]] to build note-to-note connections
• Multiple LLM Support: Works with Claude, OpenAI, Gemini, and local servers — Ollama plus anything OpenAI-compatible (llama.cpp, LM Studio, vLLM)
• Reasoning Effort Control: Tune how hard the model thinks, separately for extraction and Smart Search
• Korean Language Support: Bigram Jaccard similarity for robust Korean text matching (handles particles and spacing variations), with all names normalized to Unicode NFC so composed and decomposed Hangul resolve to the same entity
• Interactive Graph View: Visualize your knowledge graph with a ForceAtlas2 layout — the force model Gephi uses — so clusters read as clusters and every label has room
• Large Graph Support: Optimized for thousands of nodes with fast rendering
• Note Neighborhood Panel: See connections for the current note in a sidebar
• Manual Entity Merge: Merge duplicate entities via graph view context menu
• Quick Access: Ribbon icon menu for common actions
• Status Bar: Real-time graph statistics display

Entity Resolution

A key insight from recent knowledge graph research is that entity resolution is critical for quality knowledge graphs [3]. Without proper deduplication, "AI", "artificial intelligence", and "Artificial Intelligence" appear as separate nodes, fragmenting your knowledge.

Simple Graph Builder uses a hybrid resolution pipeline (opt-in feature):

Stage	Method	Speed
1. Persistent cache	Previously resolved tokens	O(1)
2. Session cache	Same name resolved this session	O(1)
3. Exact name	Hash lookup on canonical name	O(1)
4. Alias match	Hash lookup on stored aliases	O(1)
5. Embedding similarity	Cosine similarity > 0.90 = auto-merge	O(n)
6. LLM verification	Ambiguous matches (0.80-0.90) verified by LLM	API call
7. Create new	No match found	-

This approach resolves most entities via fast hash lookups, reserving expensive embedding searches and LLM calls for genuinely ambiguous cases.

Commands

Command	Description
Analyze current note	Extract entities from the active note
Search related notes	Find notes by entity name (exact/fuzzy match)
Smart Search (AI)	Natural language search using LLM to explore the graph
Open graph view	Show the knowledge graph visualization
Open note neighborhood panel	Show current note's connections in sidebar
Remove current note from graph	Remove active note from the graph
Rebuild note layer	Recreate note nodes and their links from existing data (no API calls)
Clear all graph data	Reset the entire graph

Data Model

Entity Types (10 Fixed Types)

The LLM must classify each entity into one of these types:

Type	Description	Examples
PERSON	People, individuals	Authors, researchers, team members
ORGANIZATION	Companies, institutions	Google, MIT, research labs
CONCEPT	Ideas, theories, principles	Machine learning, API design
PROJECT	Projects, products, initiatives	Obsidian, GraphRAG
TOOL	Software, hardware, instruments	Python, VS Code, Docker
EVENT	Meetings, conferences, milestones	NeurIPS 2024, sprint review
PLACE	Locations, venues, geography	San Francisco, AWS us-east-1
DOCUMENT	Papers, books, articles, notes	"Attention Is All You Need"
METHOD	Techniques, approaches, workflows	Agile, TDD, fine-tuning
TOPIC	Subjects, themes, fields, domains	NLP, distributed systems

One further type, NOTE, is created by the plugin rather than the LLM. Each analyzed note becomes a NOTE node that mentions the entities extracted from it and links to the notes it wikilinks, which is what ties separate notes into one graph. Turn them off with Show note nodes for an entity-only view.

Relationships (Free-form Verbs)

Relationships are expressed as active verbs describing how entities relate:

Verb Examples	Meaning
develops, creates, builds	Creation, authorship
uses, applies, implements	Usage, application
causes, leads to, enables	Causality, dependency
contains, includes, has	Composition, membership
cites, references, based on	Citation, source
relates to, similar to	General association

Each relationship also includes an optional detail field for additional context.

UI Elements

Ribbon Icon

Click the graph icon in the left ribbon to access:

• Analyze current note
• Open graph view

Status Bar

Shows real-time graph statistics with node counts by label.

Note Neighborhood Panel

A sidebar panel showing:

• Extracted Nodes: Entities from the current note with entity type badges
• Connected Nodes: Grouped by entity type (PERSON, CONCEPT, TOOL, etc.)
• Relationships: Shows relationship verb and detail for each connection
• Click nodes to see source notes and relationship details

Graph View Context Menu

Right-click a node to:

• Merge into...: Manually merge duplicate entities (source becomes alias of target)

Settings

API Configuration

• API Provider: Choose between Claude, OpenAI, Gemini, or Ollama (local)
• API Key: Stored per provider, so extraction and Smart Search can use different providers without one overwriting the other's key. Not needed for a local server unless it was started with --api-key.
• Server API (local only): Which API the local server speaks — Ollama (/api/chat) or OpenAI-compatible (/v1/chat/completions). Use OpenAI-compatible for llama.cpp's llama-server, LM Studio, vLLM and similar; set Host to the base address without the /v1 suffix.
• Model: Select or enter a custom model name

Analysis Settings

• Extraction Mode: Control extraction depth
  • Standard: Max 15 entities per chunk (fast, low cost)
  • Thorough: No limits per chunk (comprehensive extraction)
• Reasoning effort: How much the model thinks before extracting — Auto, Minimal, Low, Medium, High, or Max. Defaults to Minimal: notes are processed in many parallel chunks, so higher levels raise cost and latency noticeably. Models that don't support the setting (such as claude-haiku-4-5) are flagged in settings and simply ignore it.
• Chunked Processing: Long notes are automatically split into ~500 token chunks and processed in parallel (max 3 concurrent)
• Auto-analyze on save: Automatically analyze notes when you save them (2-second debounce)
• Analyze entire vault: Batch analyze all notes with progress tracking and cancellation support

Smart Search Model

You can configure a separate model for Smart Search queries, allowing you to use faster/cheaper models for extraction while using more capable models for search:

• Use separate model for smart search: Enable to configure a different model
• Smart search provider: Choose provider (Claude, OpenAI, Gemini, Ollama)
• Smart search model: Select or enter a custom model name
• Smart search reasoning effort: Set independently from extraction — searching benefits from more reasoning than extraction does
• API key: Shown when Smart Search uses a different provider than extraction, since that provider's own settings block is hidden

This is useful for optimizing cost vs. quality - e.g., use gpt-5.4-mini for extraction and gpt-5.6-luna for search.

Entity Resolution (Opt-in)

Enable embedding-based entity resolution for intelligent deduplication:

• Enable embeddings: Turn on the hybrid resolution pipeline
• Embedding provider: OpenAI, Gemini, or a local server — chosen independently of the chat provider, so a local chat model does not force local embeddings
• Embedding server API (local only): Ollama (/api/embed) or OpenAI-compatible (/v1/embeddings), set separately from the chat provider's API
• Embedding server host (local only): leave blank to reuse the chat provider's host; set it when embeddings run elsewhere
• Embedding API key: Separate key for embedding API calls
• Embedding model:
  • OpenAI: text-embedding-3-small (1536 dims), text-embedding-3-large (3072 dims)
  • Gemini: gemini-embedding-001 (768 / 1536 / 3072 dims)
  • Ollama: nomic-embed-text (768 dims), mxbai-embed-large (1024 dims)
• High confidence threshold: Auto-merge above this similarity (default: 0.90)
• Low confidence threshold: LLM verification range floor (default: 0.80)
• Enable LLM verification: Verify ambiguous matches with LLM calls
• Compute embeddings: Generate embeddings for existing nodes
• Clear resolution cache: Reset learned token mappings

View Settings

• Open graph in main window: Toggle to open the graph visualization in a main tab instead of the right sidebar
• Show note nodes: Include your notes in the graph alongside the entities they mention. Turn off for an entity-only view
• Minimum connections: Hide nodes with fewer than this many connections

Data Management

• View graph statistics (nodes by entity type, total relationships)
• Clear all graph data

Supported Models

Note analysis requires a model that can return structured output (JSON schema). Models that cannot are refused with a message rather than silently producing a lower-quality graph, and the settings panel flags them as you select them.

Provider	Models
Claude	claude-sonnet-5, claude-haiku-4-5
OpenAI	gpt-5.6-luna, gpt-5.4-mini
Gemini	gemini-3.6-flash, gemini-3.5-flash-lite
Local	any model your server exposes — Ollama, or an OpenAI-compatible server such as llama.cpp's llama-server, LM Studio or vLLM

Any other model can be typed into the Custom… field. Smart Search additionally needs tool calling; for local servers, start llama-server with --jinja, and prefer qwen3:* or gpt-oss:* on Ollama.

Upgrading to 0.5.0

This release fixes a bug that made large graphs dense and slow to load, and repairs the damage automatically on first load. Nothing is re-analyzed and no API calls are made.

• Redundant link edges are removed. Wikilinks used to connect every entity in a note to every entity in each linked note, which grows as the square of the entities per note. One 141-note vault carried 188,097 such edges out of 191,436 — 98% of its graph, in a 115 MB data file. They are deleted on load.
• Notes become nodes. Each analyzed note now appears as a NOTE node that mentions its entities and links to the notes it wikilinks — one edge per link, as intended. The note layer is rebuilt from Obsidian's own link index. Turn it off with Show note nodes, or rebuild it any time with the Rebuild note layer command.
• Duplicate Korean entities are merged. Names were compared without Unicode normalization, so composed (NFC) and decomposed (NFD) Hangul — identical on screen, and what macOS puts in file paths — produced two separate nodes for one concept, and made Korean search miss. Names are now normalized to NFC everywhere, and existing duplicates are folded together, keeping both notes' references and the alternate spelling as an alias.
• Rendering is faster. The graph view uses WebGL where available, budgets edges as well as nodes, hides labels when zoomed out, and simplifies edges on large graphs.

The same vault above went from 191,436 edges / 115 MB to 7,449 edges / 6.3 MB, with average connections per node dropping from 178 to 6.6.

Upgrading to 0.4.0

This release moves to each provider's current API. Two things happen automatically on first load:

• Model IDs are migrated. Retired IDs are rewritten to their current equivalents (for example claude-sonnet-4-5-20250929 → claude-sonnet-5, gpt-4o → gpt-5.6-luna). Ollama model names are left alone, since those refer to models you have pulled locally. Check your model selection afterwards if you had a specific one configured.
• Gemini embeddings are reset. text-embedding-004 was shut down in January 2026, so it is replaced by gemini-embedding-001. Stored embeddings from the old model are discarded and you will be prompted to recompute them; entity resolution is paused until you do. OpenAI and Ollama embeddings are unaffected.

Installation

From Obsidian Community Plugins

1. Open Settings → Community plugins
2. Search for "Simple Graph Builder"
3. Click Install, then Enable

Using BRAT (Recommended for Beta)

1. Install BRAT from Community Plugins
2. Open command palette → "BRAT: Add a beta plugin"
3. Enter: junhewk/simple-graph-builder
4. Enable the plugin in Settings → Community plugins

Manual Installation

1. Download main.js, styles.css, and manifest.json from the latest release
2. Create folder: VaultFolder/.obsidian/plugins/simple-graph-builder/
3. Copy the downloaded files into the folder
4. Reload Obsidian and enable the plugin

Usage

Quick Start

1. Configure your API key in Settings → Simple Graph Builder
2. Open a note and run command: Analyze current note
3. View results with command: Open graph view

Graph View

• Click a node to highlight its connections
• Double-click a node to open search with that term
• Right-click a node to access merge options
• Hover on edges to see relationship type and detail
• Click the background to reset highlights
• Scroll to zoom in/out
• Drag to pan around the graph

Node colors are determined by entity type (10 predefined colors). Edges use unified gray styling with relationship verbs shown on hover.

Layout

Graphs are laid out with fCoSE, then refined so the result is readable at vault scale:

• Above 1000 nodes fCoSE runs in its fast spectral mode and ForceAtlas2 — the force model Gephi uses — does the actual force work. Running fCoSE's own refinement at that size takes minutes; this takes about three seconds on a 2263-node vault.
• Every graph then gets a spacing pass that scales the layout out and separates whatever still overlaps. This matters below 1000 nodes too: fCoSE alone packs an 871-node graph tightly enough that only 5% of nodes have space for their label.

How much space that pass aims for depends on how big the graph is. Small graphs get the full width of a label, so nothing collides at the zoom they open at. Large ones get less: the whole layout is fitted to the pane, so spacing every node a label apart makes a 5000-node graph so wide that each node lands on a fraction of a pixel and the view looks empty. Those are read by zooming in, where the tighter spacing is still ample.

Edges follow the same logic. Zoomed out they are drawn bold, because a 1px line covers a fraction of a pixel there and only the mass of them registers; zoom in and they thin out so they sit behind the nodes and labels rather than across them.

The result is a graph of distinct clusters rather than one dense block. If yours still looks crowded, raise Minimum connections or turn off Show note nodes to thin it out.

Search

Two search modes are available:

Basic Search

1. Run command: Search related notes
2. Enter a concept or entity name
3. Toggle Exact match for precise matching
4. Click results to navigate to notes

Smart Search (AI)

1. Run command: Smart Search (AI)
2. Enter a natural language question (e.g., "What methods did we use for the recommendation project?")
3. The LLM explores the graph using tool calls, following multiple paths
4. View the AI-generated answer with relevant nodes and source notes
5. Click source note links to navigate

Note: Smart Search requires models with tool calling support. Some Ollama models (deepseek-r1:*, gemma3:*) have limited support. Recommended: qwen3:*, gpt-oss:* for Ollama.

API Costs

This plugin makes API calls to extract entities from your notes.

• Claude, OpenAI, Gemini: Each note analysis and Smart Search query will incur API costs based on your provider's pricing
• Ollama: Free (runs locally on your machine)

Embedding Costs (if enabled)

• OpenAI: ~$0.02 per 1M tokens for text-embedding-3-small
• Gemini: Free tier available for gemini-embedding-001
• Ollama: Free (local models like nomic-embed-text)

Consider using Ollama for cost-free operation, or batch analyze during off-peak hours to manage costs.

Privacy

• Your notes are sent to the configured LLM provider for entity extraction
• No data is stored externally; all graph data stays in your vault
• Consider using Ollama for fully local, private processing
• Embeddings are stored locally in binary format (embeddings.bin)

If you version-control your vault

Obsidian stores plugin settings — including your API keys — in .obsidian/plugins/simple-graph-builder/data.json, together with the graph itself. If your vault is a git repository, add this to your .gitignore:

.obsidian/plugins/simple-graph-builder/data.json

Pushing that file to a public repository publishes your keys in plaintext, and deleting it later does not help — git keeps the history. If it has already been pushed, revoke the key at your provider's console and issue a new one.

Technical Background

This plugin's entity resolution approach is inspired by recent advances in knowledge graph construction:

• LightRAG [1] demonstrated lightweight graph-based RAG but lacks entity resolution
• Microsoft GraphRAG [2] provides comprehensive extraction but at high cost ($50-100+ per corpus)
• KGGen [3] introduced the insight that entity resolution is critical for quality knowledge graphs

Simple Graph Builder combines the simplicity of LightRAG with KGGen's hybrid resolution approach, adapted for Obsidian's local-first architecture.

Development

npm install
npm run dev     # watch build
npm run build   # production build (typecheck + bundle)
npm test        # provider wire-level tests
npm test -- gemini   # run one suite
npm run eval    # live end-to-end check against the real provider APIs

npm test bundles each tests/*.test.ts with esbuild, stubbing Obsidian's requestUrl so outgoing requests can be captured, then asserts the exact JSON each provider adapter builds. No test framework is involved — esbuild is already a dev dependency, and the plugin ships its whole bundle.

These are deliberately wire-level, because that is where the bugs are: a parameter a model rejects, a tool result dropped from a loop, embeddings written at the wrong vector width. Each suite exits non-zero on failure, and the release workflow runs them before publishing.

tests/layout.test.ts is the exception: it scores the graph layout instead of asserting a payload. It generates a vault-shaped graph, lays it out headlessly, and measures how many nodes are individually visible, how many have room for their label, how long edges are relative to typical node spacing, and how well clusters separate — against thresholds and against the layout the previous release shipped. To see the numbers at real-vault scale, bundle it and run it directly:

npx esbuild tests/layout.test.ts --bundle --platform=node --outfile=/tmp/layout.cjs
SGB_LAYOUT_BENCH=1 node /tmp/layout.cjs

npm run eval is the opposite end: it bundles tests/*.eval.ts against a stub whose requestUrl performs real HTTP, then runs the full extraction pipeline against every provider you have a key for in the environment. Providers without a key are skipped, so it is safe to run with just one.

ANTHROPIC_API_KEY=... OPENAI_API_KEY=... GEMINI_API_KEY=... npm run eval

References

[1] Guo, Z., et al. (2024). "LightRAG: Simple and Fast Retrieval-Augmented Generation." https://github.com/HKUDS/LightRAG

[2] Edge, D., et al. (2024). "From Local to Global: A Graph RAG Approach to Query-Focused Summarization." arXiv:2404.16130. https://github.com/microsoft/graphrag

[3] Shu, Y., et al. (2025). "KGGen: Extracting Knowledge Graphs from Plain Text with Language Models." NeurIPS 2025. arXiv:2502.09956. https://github.com/stair-lab/kggen

[4] Neo4j, Inc. (2024). "Neo4j GraphRAG Package for Python." https://neo4j.com/docs/neo4j-graphrag-python/current/

[5] Veen, A. (2024). "pgvector: Open-source vector similarity search for Postgres." https://github.com/pgvector/pgvector

Support

• GitHub Issues
• Documentation

License

MIT License - see LICENSE for details.