Protégé coexistence¶
Guide for teams using Protégé today and evaluating Strixonomy v0.26. A first-week migration guide ships today. RDF/XML and OWL/XML write-back shipped in v0.21 (semantic re-serialize, not byte-identical); v0.22 completes OWL 2 authoring depth; v0.23 adds realization, instance checking, and SWRL; v0.24 adds DL Query — see OWL/XML write-back, DL Query, What ships today, and roadmap.
Canonical capability matrix: What ships today. Decision matrix: Protégé vs Strixonomy. Gap analysis for adopters: Known limitations.
Use Strixonomy for (v0.26)¶
| Workflow | Status |
|---|---|
| Browse ontologies in VS Code | Shipped |
| Edit labels, comments, parents in Turtle | Shipped |
| Edit OBO terms (name, synonyms, defs, is_a, …) | Shipped (engine v0.12; inspector v0.13) |
| Edit RDF/XML / OWL/XML (core inspector + patch ops) | Shipped (v0.21; semantic re-serialize) |
Complex SubClassOf / EquivalentClasses / disjoint (Manchester) | Shipped (richest on Turtle) |
| Property chain editing | Shipped (v0.12) |
| Workspace refactoring (rename, migrate namespace, move, extract) | Shipped (Turtle; preview + apply) |
| SQL/SPARQL queries over workspace | Shipped |
| DL Query (Workbench DL mode, CLI, LSP) | Shipped (v0.24+) — honesty notes |
| Graph visualization (class, property, import, neighborhood, and v0.26 kinds) | Shipped |
CI lint (strixonomy validate) | Shipped — suitable for production CI |
| EL/RL/RDFS/DL classification | Shipped |
OWL 2 DL classification (dl / auto profiles) | Shipped (OntoLogos 1.x; not certified HermiT-identical) |
| Realization / instance checking (ABox) | Shipped (v0.23) |
| SWRL rule browser / editor / validate | Shipped (v0.23; DLSafe) |
| Inferred hierarchy toggle | Shipped (after reasoner run) |
OBO format index + obo_id in explorer | Shipped |
ROBOT CLI in CI (strixonomy robot) | Shipped (requires Java + robot on PATH) |
| Multi-root VS Code workspaces | Shipped (all folders indexed) |
| Semantic diff (CLI / LSP / panel) | Shipped |
| Plugin SDK 1.0 (manifest, lifecycle, providers) | Shipped (v0.26) |
Keep Protégé for (today)¶
| Workflow | Why |
|---|---|
| HermiT-identical DL explanations / certified HermiT results | OntoLogos DL is not certified HermiT-identical |
| Exact Protégé DL Query tab / Manchester fidelity expectations | Strixonomy ships DL Query (v0.24+) with documented honesty limits — dual-check critical queries if you require Protégé+HermiT identity |
| Full OWL 2 DL axiom catalog for all formats | Partial Manchester + patches — see SHIPPED and known limitations |
| Byte-identical OWL/XML or RDF/XML layout | Strixonomy re-serializes for semantic fidelity (ADR-0021) |
| Workflows that depend on Protégé-specific plugins | Not replicated; Strixonomy uses subprocess SDK 1.0 — not a Protégé plugin host |
Practical split workflow¶
- Author routine Turtle, OBO, and light XML changes in VS Code (inspector, Manchester editor, refactoring, patches)
- Validate in CI with
strixonomy validateand optionallystrixonomy classify --profile el - Run ROBOT in CI when needed — ROBOT interop
- Keep Protégé for Protégé-only plugins, byte-identical XML, or uncovered axiom types
- Prefer Turtle when you need byte-stable diffs or refactor apply
Round-trip tips¶
- After Protégé saves XML, re-index in Strixonomy; expect layout differences, not semantic loss for edited entities/labels/parents/imports.
- Prefer Turtle for shared team authoring when Git diffs must stay readable.
- See OWL/XML write-back for supported XML patch ops.