Documentation

Learn how to use OntoKit to create, edit, and collaborate on OWL ontologies.

Getting Started

OntoKit is a modern, collaborative OWL ontology curation platform designed as a replacement for Stanford WebProtege. It provides a streamlined workflow for creating, editing, and managing semantic web ontologies.

Quick Start

Browse public projects without signing in, or sign in to create and contribute
Create a new project or join an existing one
Upload an ontology file (Turtle, RDF/XML, OWL/XML) or start from scratch
Use the form-based editor to browse and modify classes, properties, and individuals
Changes are auto-saved as drafts; navigate away to commit them to git
Create branches and pull requests, or submit suggestions for review

Core Concepts

Projects

Projects are containers for your ontologies. Each project has its own Git repository for version control, team members, and access settings.

Branches

Work on changes in isolated branches without affecting the main ontology. Merge changes through pull requests when ready.

Pull Requests

Propose changes to the ontology through pull requests. Review semantic diffs, discuss changes, and merge when approved.

Suggestions

Suggesters can propose changes without direct edit access. Suggestions are auto-saved as you work and submitted for editor review with approve, reject, or request-changes outcomes.

Linting

Automatic validation checks your ontology for common issues, missing labels, and best practice violations.

Auto-Save

A two-tier auto-save system protects your work: edits are cached locally on blur, and committed to git when you navigate away. Draft indicators show unsaved changes on tree nodes.

Team Roles & Permissions

Each project member is assigned a role that determines what they can do. Roles are project-scoped — a user can have different roles in different projects.

Role	Capabilities
Owner	Full control over the project. Can delete the project, transfer ownership, manage members and settings, create branches, edit the ontology, and run the health check.
Admin	Manage members and project settings, create branches, edit the ontology, and run the health check. Cannot delete the project.
Editor	Create branches, edit ontology source, and create pull requests. Review and approve/reject suggestions from suggesters. Cannot manage members, change settings, or run the health check.
Suggester	Propose changes via suggestion sessions that are reviewed by editors. Can browse the ontology, create and submit suggestions, and view their own suggestion history. Cannot directly edit the ontology or create branches. This is the default role for new project members.
Viewer	Browse the class tree, view the source in read-only mode, and view health check results. Cannot make any changes.

Good to know

The person who creates a project automatically becomes its Owner
New project members are assigned the Suggester role by default
Public projects can be viewed by anyone, but only members can edit
Private projects are only visible to their members

Editor Modes

OntoKit offers two editing modes to suit different workflows. Your preference is saved and persists across sessions.

Standard Mode

A form-based editing experience for classes, properties, and individuals. Edit labels, comments, annotations, and relationships through structured fields. Entities are read-only by default — click "Edit Item" to start editing, with changes auto-saved as you work.

Developer Mode

Direct access to the Turtle source with full syntax highlighting, auto-completion, and inline validation in a Monaco-based editor. Ideal for power users who prefer working with raw RDF/OWL syntax.

Editor Features

Entity Tree

Navigate your ontology using hierarchical trees for classes, properties, and individuals. Entities are organized by their subclass/subproperty relationships, with lazy loading for large ontologies.

Expand/collapse hierarchies with multi-level controls (one level, all, or none)
View subclass counts at each level
Search for entities by name or IRI
Drag-and-drop reparenting with cycle detection and undo
Right-click context menus for Add Subclass, Copy IRI, View in Source, and Delete
Draft indicators on nodes with unsaved changes
Language tags displayed as country flag emojis
Keyboard navigation with arrow keys and aria-activedescendant

Detail Panel

View and edit entity metadata through structured forms. Separate panels are provided for classes, properties, and individuals, each tailored to their specific OWL constructs.

Multi-language label and comment editing with inline annotation adder
Superclass/subclass and equivalent/disjoint relationships
Annotation properties with IRI-valued relationship editing
Property assertions for individuals
Entity history tab with revision tracking
Similar concepts panel for discovering related entities
Cross-references panel showing where an entity is used
Delete impact analysis before entity removal
Resizable panel dividers for customizing the layout

Graph Visualization

Explore ontology relationships visually with an interactive graph view powered by React Flow and ELK layout.

Depth-2 neighbor fetching with expandable nodes
Custom node styling for focus, parent, child, equivalent, and disjoint classes
Color-coded edges for different relationship types with hover labels
Root nodes highlighted with distinct amber/gold styling

Source Editor

Edit your ontology directly in Turtle syntax with full syntax highlighting, auto-completion, and inline validation. Available in Developer mode or via the Source tab.

Turtle syntax highlighting
Hover over IRIs to see full definitions
Ctrl+Click to navigate to class definitions or open external IRIs in a new tab
Real-time linting with inline error markers

Keyboard Shortcuts

Shortcut	Action
Ctrl+S / Cmd+S	Save current drafts
Ctrl+N / Cmd+N	Create a new entity
?	Show keyboard shortcuts help
Escape	Close overlays and dialogs

Supported Formats

Format	Extension	MIME Type
Turtle	.ttl	text/turtle
RDF/XML	.rdf, .xml	application/rdf+xml
OWL/XML	.owl	application/owl+xml
N-Triples	.nt	application/n-triples
JSON-LD	.jsonld	application/ld+json

Import & Normalization

Canonical Turtle Format

When you import an ontology file, OntoKit normalizes it to a canonical Turtle format. This ensures consistent formatting across all edits and produces minimal, meaningful diffs in version history. The normalization happens once at import time.

What changes during normalization:

All formats (RDF/XML, OWL/XML, N3, JSON-LD) are converted to Turtle (.ttl)
Triples are reordered into a consistent, deterministic sequence
Unused namespace prefixes may be removed (e.g., rdf:, xml:, xsd: if not explicitly used)
Whitespace and formatting are standardized
The shorthand a is used for rdf:type

Metadata Synchronization

When you update a project's name or description in Project Settings, OntoKit automatically syncs these changes to the ontology's RDF metadata properties.

How metadata sync works:

Title: Updates dc:title, dcterms:title, or rdfs:label (whichever exists)
Description: Updates dc:description, dcterms:description, or rdfs:comment
If no metadata property exists, dc:title / dc:description is added
Changes are committed to git with a descriptive message

API Reference

OntoKit provides a comprehensive REST API for programmatic access to all platform features. Use the API to integrate OntoKit with your existing tools and workflows.

View API Documentation