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OWL/XML and RDF/XML write-back

Status: Write-back shipped in v0.21; v0.22 expands OWL 2 mutate/authoring ops. Open → edit → save → reload without semantic loss for .owl/.rdf (RDF/XML) and .owx (OWL/XML). Write-back uses Horned full-document re-serialize (not byte-identical formatting). See ADR-0021.

Strixonomy indexes and edits RDF/XML and OWL/XML via Horned-OWL. The Entity Inspector marks these documents editable when parse status is OK.

Canonical capability matrix: What ships today.

What works today

Capability .owl / .rdf (RDF/XML) .owx (OWL/XML)
Workspace indexing Yes Yes
Explorer / SQL / SPARQL Yes Yes
Entity Inspector (view) Yes Yes
Entity Inspector (edit) Yes (core ops) Yes (core ops)
Patch / strixonomy patch write-back Yes Yes
Manchester editor apply Limited (named ops via patches) Limited
Refactoring apply (rename / merge / replace) Yes (remap + re-serialize) Yes (remap + re-serialize)
Refactoring apply (move / extract / …) No (Turtle-first) No (Turtle-first)

Supported XML patch ops (first cut): create/delete entity, labels/comments/annotations, SubClassOf, imports, ontology/version IRI, class assertions. Unsupported ops return structured errors and leave the file unchanged.

Edit in place

  1. Open a workspace containing .owl, .rdf, or .owx files.
  2. Index the workspace; select an entity in Entity Inspector.
  3. Edit labels, parents, create/delete entities, or manage imports as you would for Turtle.
  4. Save; Strixonomy re-serializes the whole document and reindexes.

Protégé coexistence

Protégé may rewrite XML layout on save. Strixonomy verifies semantic round-trips (entities, labels, parents, imports), not byte-identical XML. See Protégé coexistence and ADR-0021.

When to prefer Turtle

Keep Turtle (span surgery) when you need byte-stable formatting, property characteristics, complex Manchester expressions, or Turtle-first refactor ops (move / extract / ontology merge / flatten / cleanup). Rename / merge / replace also work on RDF/XML and OWL/XML.

VS Code behavior

  1. Open a workspace containing .owl / .rdf / .owx.
  2. Run Strixonomy: Index Workspace.
  3. Select an entity — edit controls are enabled for supported operations.
  4. Unsupported ops surface clear diagnostics (no silent truncate).

CLI

strixonomy validate /path/to/ontologies
strixonomy patch path/to/file.owl patches.json
strixonomy patch path/to/file.owx patches.json --preview

Patch JSON uses the same Turtle-shaped PatchOp wire format for XML documents.

Migration from earlier releases

Topic Guide
Format policy Authoring
OBO write-back OBO authoring
Protégé gaps Protégé decision guide
Serializer policy ADR-0021