OBO & ROBOT Interop Specification (v1.0)¶

Status: Target design for remaining interop. Do not implement from this page as product truth.

Shipped today: OBO index + write-back, ROBOT CLI wrappers, OBO workflows — see What ships today, OBO workflows, and ROBOT interop. Historical P0 framing: PROTEGE_PARITY.md.

Strixonomy does not reimplement ROBOT or ODK — it wraps the official ROBOT CLI today and integrates external workflow plugins (such as owlmake) for future Java-free pipelines.

1. Purpose¶

Enable biomedical ontology maintainers to use Strixonomy as a primary IDE alongside standard OBO/ROBOT/ODK release pipelines.

2. Strategy summary¶

Layer	What it does	Status
`strixonomy-robot`	Thin wrapper around the official ROBOT Java CLI	Shipped (v0.7)
Strixonomy diagnostics	Built-in lint and parse checks	Shipped
owlmake (external)	Rust-native portable ROBOT/ODK-style workflows	Reference plugin (v1.0 integration target)
Strixonomy core	Does not reimplement ROBOT merge/template/report or ODK Makefile logic	By design

Strixonomy should integrate with the ontology toolchain, not absorb it. See PLUGIN_SPEC.md.

3. OBO format (P0)¶

Parser / writer¶

Read and write OBO Format 1.4 (.obo) via fastobo + fastobo-owl (DEPENDENCY_MATRIX.md)
Validate with fastobo-validator where applicable
Map OBO ids to IRIs in catalog (obo_id, iri, namespace)
Support synonymtypedef, property_value, xref in catalog annotations table

UI¶

Explorer shows OBO shorthand ids where applicable
Manchester / completion resolves OBO ids in biomedical workspaces
Syntax highlighting for .obo files in VS Code

Milestone¶

v0.7b — OBO format support before v1.0.

4. ROBOT interop (P0) — current path¶

Thin CLI wrappers in strixonomy-robot crate (strixonomy robot subcommand):

strixonomy robot validate ./ontology
strixonomy robot merge --inputs a.owl b.owl --output merged.owl
strixonomy robot report ./ontology --report report.tsv

Requirements¶

Detect robot on PATH; clear error if missing with install link
Pass through exit codes for CI
Optional strixonomy.robotPath setting (workspace-trusted, like lspPath)

Documentation¶

Side-by-side: Strixonomy diagnostics vs ROBOT validate / report
When to use Strixonomy-only CI vs ROBOT-only vs both

5. owlmake — future external integration path¶

owlmake provides Rust-native, portable ROBOT/ODK-style workflow execution. It is a reference external workflow plugin, not a core Strixonomy crate.

Strixonomy IDE
     │
     ▼
Strixonomy (index, diagnostics, LSP)
     │
     ├── strixonomy-robot ──► ROBOT CLI (Java)     ← shipped today
     │
     └── owlmake plugin ──► Rust-native workflows ← v1.0 integration target

Integration goals (v1.0)¶

Goal	Description
Import existing ODK projects	Recognize `src/ontology/`, catalog files, import structure
Run project QC	Execute QC steps; surface results as Strixonomy diagnostics
Run release workflows	Trigger build/release pipelines from IDE or CLI
Inspect build outputs	Index and browse release artifacts in Strixonomy
Surface workflow errors	Map owlmake/ROBOT failures to Problems panel diagnostics

Clarifications¶

strixonomy-robot wraps the current ROBOT CLI — this remains the supported path when Java + robot are available.
owlmake may provide future Java-free workflow execution for teams that want portable Rust tooling.
Strixonomy must not reimplement all of ROBOT/ODK internally; plugins and CLI wrappers delegate to established semantics.
Strixonomy surfaces workflow actions; Strixonomy hosts plugin APIs; owlmake implements workflow automation.

See PLUGIN_SPEC.md for WorkflowPlugin / BuildPlugin interfaces.

6. OBO/ODK project workflow goals (v1.0)¶

Workflow	Strixonomy / Strixonomy role
Open ODK repo	Index standard layout; show imports and modules in explorer
Edit source `.ttl` / `.obo`	Turtle and OBO write-back (v0.12); RDF/XML read-only in VS Code
Run QC	`strixonomy validate` + ROBOT `report` + owlmake QC plugin
Run release	owlmake or ROBOT via plugin/CLI; inspect outputs in workspace
CI gates	`strixonomy validate`, `strixonomy classify`, `strixonomy robot validate`

7. Example workspace¶

examples/obo-workflow/ — minimal mixed OBO + OWL repo demonstrating:

Edit in Strixonomy
strixonomy validate + strixonomy robot validate in CI
strixonomy robot merge for release

8. Non-goals¶

Reimplementing ROBOT merge/template/report logic inside Strixonomy
Replacing ODK Makefile or owlmake with built-in Strixonomy code
OBO Foundry automated compliance as a core feature (P1 validator plugin)

9. Parity tracking¶

See PROTEGE_PARITY.md — OBO & biomedical section.