Back to AI Education
Open Knowledge Format Workflow

Transform PDF Collections into an Interactive AI Knowledge Graph

This guide walks you step-by-step through setting up an OKF (Open Knowledge Format) bundle using Claude Code in your terminal, while using Obsidian as a real-time interactive visual graph browser.

Customize Prompt Variables

Type your specific folder name below to automatically update all prompt templates on this page.

1

Directory Structure & Obsidian Setup

Set up your vault directory structure. The okf/ folder acts as your centralized knowledge bundle, keeping generated summaries distinct from your raw PDF files.

// Recommended Vault Layout
MedEd-Vault/
├── MedEd/ (Place raw PDF files here)
│ ├── article_1.pdf
│ └── article_2.pdf
└── okf/ (Subfolder for AI Knowledge Bundle)
├── index.md (Root Table of Contents)
├── log.md (Chronological update log)
├── articles/ (OKF type: article summaries)
└── concepts/ (OKF type: concept thematic nodes)

Configure Obsidian Settings

  1. Open Obsidian and select "Open folder as vault" → Choose MedEd-Vault.
  2. Go to Settings (Cmd/Ctrl + ,) → Files and links.
  3. Set New link format to Relative path to file.
  4. Toggle Detect all file extensions to ON so PDFs are visible in your sidebar.
2

Execute Batch Generation via Claude Code

Open your system terminal, navigate to your vault folder, launch Claude Code, and paste the sequential prompts below.

Terminal Command
cd /path/to/MedEd-Vault && claude
Prompt 1: Convert PDFs to OKF Articles
Read all PDF files inside `./MedEd/`. For each article, generate a dedicated OKF Markdown file in `./okf/articles/` named `YYYY-author-topic.md` following this frontmatter format: --- type: article title: "<Article Title>" description: "<1-2 sentence executive summary>" tags: [meded, ai, research] timestamp: 2026-07-27 resource: file://MedEd/<filename>.pdf --- Include these structured sections in each file: 1. # Executive Summary & Objectives 2. # Key Findings & Frameworks 3. # Methodology & Educational Context 4. # Challenges & Future Directions 5. # Related Concepts (leave empty for now)
Prompt 2: Synthesize Concept Nodes & Graph Edges
Analyze all files in `./okf/articles/`. Identify core overlapping themes across the papers. 1. Create dedicated OKF concept nodes in `./okf/concepts/` using `type: concept` in the frontmatter. 2. In each concept file, summarize the overarching theme and add relative Markdown links back to supporting articles in `./okf/articles/`. 3. Update the `# Related Concepts` section in each article in `./okf/articles/` with relative links pointing to these concept nodes. 4. Create `./okf/index.md` with `type: index` linking to all articles/concepts, and log initial creation in `./okf/log.md`.
3

Obsidian Visual Graph & Color Rules

Open Graph View in Obsidian (Cmd/Ctrl + G). Click the Gear Icon (Display Settings) to customize your visual view:

Graph Search Filter

Paste this string into the Graph Filters → Search box to eliminate hub starbursts and root file noise:

-[type: index] -file:CLAUDE.md -path:.claude
Graph Groups (Color Coding Nodes)

Click New Group under the Groups tab and enter these exact queries:

Articles (Blue)
line:("type: article")
Concepts (Green)
line:("type: concept")

Pro-Tip: Globally Exclude CLAUDE.md from Obsidian

Go to Settings → Files and links → Excluded files → Add CLAUDE.md. This completely hides the configuration file from your visual graph and quick switcher while allowing Claude Code in terminal to read it natively.

4

Incremental Batch Updates

When you drop new PDFs into MedEd/, you don't need to process them manually. Save this workflow file inside your vault as CLAUDE.md:

File: ./CLAUDE.md
# Project Workflows ## /update-okf When I ask to "update OKF" or execute this command: 1. Scan `./MedEd/` for new PDFs not yet summarized in `./okf/articles/`. 2. Generate OKF summaries for new papers using `type: article`. 3. Re-evaluate concepts in `./okf/concepts/` and cross-link new articles. 4. Update `./okf/index.md` and append a summary entry in `./okf/log.md`.

Next time you add papers, simply open terminal and type: update OKF in Claude Code.

5

Backing Up Your Vault to GitHub

Keep your knowledge graph safe and version-controlled on GitHub. Create a .gitignore file first to prevent temporary cache files from cluttering your commit history.

File: ./.gitignore
.obsidian/workspace.json .obsidian/workspace-mobile.json .obsidian/plugins/obsidian-git/data.json .DS_Store Thumbs.db
Git Push Terminal Commands
git init
git add .
git commit -m "Initial OKF Knowledge Graph backup"
git branch -M main
git remote add origin https://github.com/YOUR_USERNAME/MedEd-Vault.git
git push -u origin main
Copied to clipboard!