Migrating from Protégé — first week

This guide helps ontology teams adopt OntoCode v0.13 alongside or instead of Protégé. For a capability comparison, see Protégé vs OntoCode and What ships today.

Before you start

OntoCode fits well when you:

• Version-control ontology files (Turtle, OWL, OBO) when your team uses shared repositories
• Want VS Code editing, CI validation, and semantic diff
• Can edit Turtle (.ttl) or OBO (.obo) for write-back (RDF/XML and JSON-LD are read-only in the inspector)

Keep Protégé (for now) when you need:

• OWL/XML or RDF/XML in-place editing
• A full DL axiom catalog UI for every axiom kind and format
• Desktop-only workflows with no Git/CI requirement
• Protégé-specific plugins

Many teams use both: Protégé for heavy axiom authoring, OntoCode for browse, lint, diff, and CI validation. See Protégé coexistence.

Day 1 — Install and open your project

1. Install OntoCode from the Marketplace or Open VSX.
2. File → Open Folder… and select your ontology repository (not a single file).
3. Trust the workspace when prompted.
4. Open the OntoCode 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 OntoCode

In Protégé	In OntoCode v0.13
Class hierarchy tab	Classes explorer view; toggle asserted / inferred / combined after reasoner
Entity editor (labels, parents)	Entity Inspector edit section (.ttl and .obo)
DL query tab	Query Workbench — SQL catalog tables or SPARQL
Reasoner (HermiT, etc.)	OntoCode: Run Reasoner — EL/RL/RDFS/DL/auto via OntoLogos 1.0
Active ontology	All workspace folders indexed (multi-root supported)
Refactor / move axioms	Rename Entity IRI, Migrate Namespace, Move Entity, Extract Module
Diff between versions	Semantic Diff panel or ontocore diff in CI

Day 3 — Validate in CI

Add a pipeline gate so Protégé-only mistakes are caught before merge:

- run: cargo install ontocore-cli --locked --version 0.13.0
- run: ontocore validate ./src/ontologies

Optional: fail on unsatisfiable classes:

- run: ontocore classify . --profile el --format json

Full examples: CI integration.

Day 4 — Queries and diagnostics

1. Open Query Workbench → run SELECT short_name, labels FROM classes.
2. Inspect lint issues in Diagnostics and the Problems panel.
3. Export query results (CSV/JSON) for reporting.

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

Day 5 — Reasoning and hierarchy

1. Run OntoCode: Run Reasoner with profile el (or auto for DL ontologies).
2. Review unsatisfiable classes in Reasoner Results.
3. Set Hierarchy Mode to inferred or combined to see inferred parents in the explorer.

Guide: Reasoner. Profile selection: FAQ.

Week 1 checkpoint

By end of week one you should be able to:

• [ ] Browse and edit Turtle entities in VS Code
• [ ] Run ontocore validate (or classify) in CI
• [ ] Compare a branch with Semantic Diff or ontocore diff
• [ ] Document which tasks stay in Protégé vs OntoCode for your team

Common friction points

Issue	Resolution
Cannot edit OWL/XML in inspector	Convert module to Turtle for write-back, or edit in Protégé
SQL query fails	OntoCore SQL is single-table subset — use SPARQL for graph patterns
Reasoner slow or fails on DL	Check workspace limits; try el profile first
Team expects plugin ecosystem	Plugin host is v1.0 target — not installable in v0.13

Next steps

Goal	Document
Enterprise evaluation pack	Enterprise evaluation
Split workflow with Protégé	Protégé coexistence
Semantic diff for releases	Semantic diff
OBO / ROBOT pipelines	OBO workflow · ROBOT interop