Migrating from Protégé — first week¶

This guide helps ontology teams adopt Strixonomy v0.27.0 alongside or instead of Protégé. For a capability comparison, see Protégé vs Strixonomy and What ships today.

Before you start¶

Strixonomy fits well when you:

• Version-control ontology files (Turtle, OWL, OBO) in shared repositories
• Want VS Code editing, CI validation, and semantic diff
• Can edit Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), or OWL/XML (.owx) for write-back (XML is semantic re-serialize — OWL/XML write-back)
• Need Protégé-like menus, reasoner workflows, explanations, graphs, and imports in the IDE

Keep Protégé (for now) when you need:

• Byte-identical OWL/XML or RDF/XML layout after save
• A full DL axiom catalog UI for every axiom kind and format
• Protégé-specific plugins or a curated plugin marketplace (Strixonomy Plugin SDK 1.0 freezes the subprocess wire today; marketplace remains product 1.0 — Plugin policy)
• WebProtégé-style live collaboration
• HermiT-identical DL explanations (OntoLogos is not certified HermiT-identical)

Many teams use both: Protégé for heavy axiom authoring or Protégé-only plugins, Strixonomy for browse, light edit, lint, diff, reasoning, DL Query, and CI. See Protégé coexistence.

Honest desktop known gaps (v0.27.0 tagged)¶

See Versions & channels if Marketplace lags behind the GitHub Release VSIX.

Full matrix: known-limitations · SHIPPED.

Day 1 — Install and open your project¶

1. Install Strixonomy from the Marketplace or Open VSX.
2. File → Open Folder… and select your ontology repository (not a single file).
3. Strixonomy’s bundled language server works in Restricted Mode — Trust only if you set custom strixonomy.lspPath or strixonomy.robotPath.
4. Open the Strixonomy activity bar and confirm Ontologies lists your .ttl / .owl files.
5. Expand Classes and click an entity to open the Entity Inspector.

Follow the first success core path if anything is empty after trust + index.

Day 2 — Map Protégé habits to Strixonomy¶

Day 3 — Validate in CI¶

- run: cargo install strixonomy-cli --locked --version 0.27.0
- run: strixonomy validate ./src/ontologies

Optional: fail on unsatisfiable classes, or assert an instance:

- run: strixonomy classify . --profile el --format json
- run: strixonomy realize . --profile rl --format json

Full examples: CI integration · Realize cookbook.

Day 4 — Queries, imports, diagnostics¶

1. Open Query Workbench → run SELECT short_name, labels FROM classes.
2. Use Manage Imports to add/remove Turtle imports; Reload Imports after external changes.
3. Inspect lint issues in Diagnostics and the Problems panel.

SQL subset limits: SQL reference. SPARQL: SPARQL reference.

Day 5 — Reasoning, explanations, visualization¶

1. Synchronize Reasoner (reindex + classify) or Classify Ontology.
2. Review unsatisfiable classes; open Explanation and regenerate if the stale banner appears after edits.
3. Run Realize (or inspect realization in the Reasoner panel) for ABox inferred types.
4. Open Rule Browser if your ontology uses SWRL; edit or validate rules in Rule Editor.
5. Open Class Graph in asserted vs inferred mode; truncated graphs show a warning on large ontologies.
6. Set Hierarchy Mode to inferred or combined.

Guide: Reasoner · SWRL cookbook.

Week 1 checkpoint¶

• [ ] Browse and edit Turtle/OBO/XML entities in VS Code
• [ ] Run reasoner lifecycle (classify / consistency / realize / stop) and open an explanation
• [ ] Optionally open Rule Browser for SWRL (if your ontology uses rules)
• [ ] Run strixonomy validate (or classify / realize) in CI
• [ ] Compare a branch with Semantic Diff or strixonomy diff
• [ ] Document which tasks stay in Protégé vs Strixonomy for your team

Common friction points¶

Next steps¶