The periodic table of agentic biomedical research.

BioOKF, the Biomedical Open Knowledge Format, is a typed and structured open format for biomedical research. Its 28 node types and 35 relationship predicates let an AI agent curate knowledge bases that are grounded in the standardized rules and entities of biomedical science, then explore and share them in a desktop Studio.

Install BioOKF View on GitHub
Claude Code + Codex plugin Studio 0.3.0 graph export macOS, Apple Silicon & Intel Rust core, Tauri Studio Apache-2.0
The format
A Git-shippable tree of Markdown and YAML. A closed universe of 28 node types and 35 edge predicates, with node-based provenance on every claim.
The toolchain
A Rust core, the scriptable bokf CLI (23 commands), and the bokf-mcp server (33 tools). The same engine, three surfaces.
The Studio
A Tauri desktop app that renders the base as an interactive, type-colored graph, with polished zoom, fit-to-view, self-contained HTML export controls, panels, an integrated terminal, and a live agent loop.

What it is

A fixed vocabulary, not a bigger one.

BioOKF is a biomedical profile of Google Cloud's Open Knowledge Format. It keeps OKF's portable substrate, a tree of Markdown you can git ship, and adds the one thing OKF leaves open: a closed, controlled vocabulary. Think of it as a periodic table for biomedical facts, a fixed set of 28 entity types and 35 relationships that every claim is mapped into, typed, reused, and sourced.

Ingest anything

Convert a PDF, HTML, DOCX, PPTX, CSV, a URL, or inline text into immutable Markdown under raw/, the bytes you never edit.

Distill to typed concepts

An agent writes one Markdown concept doc per entity, exactly one of 28 types, reusing existing nodes instead of forking duplicates.

Provenance on every claim

Each edge carries its knowledge_level, agent_type, and a primary_source node. Quantitative claims live on edges, never prose.

Query as a graph

BM25 full-text search, node and edge stats by type and predicate, plus self-contained HTML graph export. Ask what the base knows and who backs it.

Version-controlled

Every step commits atomically and appends a dated log.md. The base compounds over time, and you can forward-restore to any point.

Lint, verify, and merge

A deterministic verify gate (lint plus structure) protects quality; merge a secondary base onto a canonical main without losing the source bytes.

See it move

The Studio, recreated in motion.

No screenshots. Each demo below is a live HyperFrames mockup: the real app's chrome, palette, and node-type colors, animated in HTML to show how Studio actually feels.

Studio · graph canvas⌘K
Loading interactive mockup…
Force-directed layoutNodes pull into place and settle; hubs grow with their degree.
Type-coloredEvery node is one of 28 types; the legend maps each family.
Honest edgesNegative not_* edges render struck; provenance edges render faint.

How the graph pulls together: a knowledge base assembling itself, counts ticking up, then a neighbor-focus beat on the hub. Studio 0.3.0 adds a compact export control for saving the whole graph as a standalone HTML view.

Studio · inspectorclick
Loading interactive mockup…
Click a nodeA detail panel pops in: type badge, frontmatter, edges grouped by predicate.
See distributionsAn "edges by predicate" histogram; for edges, effect size with a 95% CI.
Click an edgeThe panel cross-fades to the provenance triplet and quantitative attributes.

How you invoke and inspect: click any node or edge to open its sidebar panel and read its distribution of relationships and evidence.

Studio · agent + terminallive
Loading interactive mockup…
Ephemeral progressPer-file progress bars appear over the nodes an agent is writing, then vanish.
Integrated terminalThe agent drives bokf in a real PTY while you watch each step.
Auto-updatesNew nodes and edges appear in the graph the moment they're written.

How the agent and you work the same base: an in-app activity banner narrates, files fill in with progress bars, and the graph updates itself, all next to the terminal.

Install

Two steps. No compiling.

Install the notarized Studio app (which bundles the CLI and MCP server), then add the plugin to connect Claude Code or Codex to those tools.

Step 1 — Studio + CLI + MCP
# Download BioOKF Studio 0.3.1 from GitHub Releases:
# BioOKF.Studio_0.3.1_aarch64.dmg  (Apple Silicon)
# BioOKF.Studio_0.3.1_x64.dmg      (Intel)
# Open it, drag BioOKF Studio to Applications.
# On first launch, accept the prompt to install
# bokf to /usr/local/bin.
Download BioOKF Studio 0.3.1 →
Step 2 — Agent plugin
# Add the marketplace, install the plugin,
# then restart Claude Code.
/plugin marketplace add Broccolito/BioOKF
/plugin install biookf@biookf

# Codex uses the side-by-side .codex-plugin manifest
codex plugin add biookf@<marketplace-name>

# Launch the visualizer:
bokf_studio_open
Want your agent to do step 2? Paste this into Claude Code: "Install the BioOKF plugin from github.com/Broccolito/BioOKF. Run /plugin marketplace add Broccolito/BioOKF, then /plugin install biookf@biookf, restart, and confirm bokf_studio_open works."
  • BioOKF Studio DMG installed (step 1 above)
  • Claude Code or Codex
  • macOS Apple Silicon or Intel: choose the matching signed DMG
  • No Gatekeeper prompts: the DMG, the .app, the CLI, and the MCP server are all Apple-notarized

What you get

Three surfaces over one engine.

The Studio, the MCP server, and the CLI all read and write a shared active base and registry, so an agent and a human can work the same knowledge base at the same time.

BioOKF Studio

A desktop app that renders a base as an interactive, type-colored graph, with node and edge detail panels, polished zoom/fit/export graph controls, self-contained HTML graph export, an integrated terminal, in-app editing, and a registry-driven sidebar of bundles that can live anywhere on disk.

bokf-mcp

A stdio MCP server: 33 tools for curation, analysis, and live control of the Studio GUI (bokf_studio_*). It ships an operating brief on initialize, so an agent knows the BioOKF rules.

bokf

The same engine as a scriptable CLI: 23 subcommands for scaffold, convert, ingest, lint, verify, query, and merge. The precise terminal surface for curation.

The live loop

The MCP server can open the Studio and drive or observe it in real time. An agent searches, selects, and navigates while you watch each action in an in-app activity banner, and reads the app's full status as JSON instead of taking screenshots.

Open source, Apache-2.0.

The format spec, the Rust toolchain, and the Studio app all live in one repository. Read the spec, file an issue, or build from source.

github.com/Broccolito/BioOKF
View on GitHub Read the docs