OBO & ROBOT Interop Specification (v1.0)

Status: target design (P0 for biomedical compete per PROTEGE_PARITY.md)

OntoCode does not reimplement ROBOT — it wraps the official CLI.

1. Purpose

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

2. 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.

3. ROBOT interop (P0)

Thin CLI wrappers in ontoindex-robot crate (or ontoindex-cli subcommand):

ontoindex robot validate ./ontology
ontoindex robot merge --inputs a.owl b.owl --output merged.owl
ontoindex 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 ontocode.robotPath setting (workspace-trusted, like lspPath)

Documentation

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

4. Example workspace

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

• Edit in OntoCode
• ontoindex validate + ontoindex robot validate in CI
• ontoindex robot merge for release

5. Non-goals

• Reimplementing ROBOT merge/template/report logic
• ODK Makefile replacement (document interop only)
• OBO Foundry automated compliance (P1 plugin)

6. Parity tracking

See PROTEGE_PARITY.md — OBO & biomedical section.