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Protégé coexistence

Interim guide for teams using Protégé today and evaluating OntoCode v0.8. A full migration guide is a v1.0 deliverable.

Canonical capability matrix: What ships today. Decision matrix: Protégé vs OntoCode. Gap analysis: Protégé parity matrix.

Use OntoCode for (v0.8)

Workflow Status
Browse ontologies in VS Code Shipped
Edit labels, comments, parents in Turtle Shipped
Complex SubClassOf / EquivalentClasses / disjoint (Manchester) Shipped
Workspace refactoring (rename, migrate namespace, move, extract) Shipped (Turtle; preview + apply)
SQL/SPARQL queries over workspace Shipped
Graph visualization (class, property, import, neighborhood) Shipped
CI lint (ontoindex validate) Shipped — suitable for production CI
EL/RL/RDFS classification Shipped
Inferred hierarchy toggle Shipped (after reasoner run)
OBO format index + obo_id in explorer Shipped (write-back: Turtle only in VS Code)
ROBOT CLI in CI (ontoindex robot) Shipped (requires Java + robot on PATH)

Keep Protégé for (today)

Workflow Why
Full OWL 2 DL reasoning (dl / auto profiles) Requires OntoLogos 1.0 — not shipped in v0.8
Property chain editing View-only in OntoCode axiom catalog until v1.0
Full OBO write-back in VS Code OBO is indexed/read-only in inspector; Turtle write-back only
Full OWL 2 DL axiom catalog Partial Manchester + patches; see Protégé parity
Editing RDF/XML or OWL/XML in place OntoCode write-back is Turtle only
Workflows that depend on Protégé-specific plugins Not replicated in OntoCode

Practical split workflow

  1. Author routine Turtle changes in VS Code (inspector, Manchester editor, refactoring, patches)
  2. Validate in CI with ontoindex validate and optionally ontoindex classify --profile el
  3. Run ROBOT in CI when needed — ROBOT interop
  4. Review DL-heavy axioms, property chains, or OBO-specific edits in Protégé when required
  5. Commit .ttl changes through Git pull requests

File format notes

  • OntoCode indexes RDF/XML, JSON-LD, OBO, and N-Triples but writes Turtle only
  • Prefer Turtle in Git for shared authoring; use Protégé round-trip when teams still maintain OWL/XML
  • Example round-trip fixtures: examples/protege-roundtrip/ in the repository

Expectations on reasoning

OntoIndex uses separate Oxigraph/Horned-OWL and OntoLogos models. Results may differ from Protégé on partial OWL mappings — check profile warnings in the Reasoner Results panel and run a pilot comparison on your corpus — Production evidence protocol.

Evaluation checklist

  1. Complete First success in 10 minutes on a representative .ttl project
  2. Run the production evidence protocol on your ontology corpus
  3. Run CI validation — CI integration
  4. Compare Protégé decision matrix and Protégé parity matrix against your requirements
  5. Review enterprise evaluation with platform/security teams