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OBO workflows

OntoIndex v0.8.0 indexes OBO Format (.obo) files and exposes obo_id in the catalog and SQL virtual tables. Write-back in VS Code remains Turtle only — OBO files are read-only in the Entity Inspector.

Canonical capability matrix: What ships today.

Prerequisites

  • OntoCode v0.8.0+ or ontoindex-cli 0.8.0+
  • Workspace containing .obo files (or mixed .obo + RDF)

Index and browse

  1. Open a folder with .obo files in VS Code.
  2. Wait for indexing (or run OntoCode: Index Workspace).
  3. Browse Classes — entities from OBO terms appear with labels; explorer may show obo_id when present.

Supported extensions: .obo (syntax highlighting included).

Query obo_id from SQL

ontoindex query /path/to/workspace "SELECT obo_id, short_name, labels FROM entities WHERE obo_id IS NOT NULL"

See SQL reference for the obo_id column.

Write-back policy

Format Index / query VS Code inspector edit ontoindex patch
.obo Yes Read-only Not supported
.ttl Yes Yes Yes

Edit OBO content with external tools or convert to Turtle for OntoCode write-back.

Example workspace

Repository example: examples/obo-workflow/

git clone https://github.com/eddiethedean/ontocode.git
cd ontocode
cargo run -- inspect examples/obo-workflow
cargo run -- query examples/obo-workflow "SELECT obo_id, labels FROM entities"

ROBOT validation

OBO pipelines often use ROBOT. See ROBOT interop guide for ontoindex robot validate and CI recipes.

Limitations

  • Minimal OBO parser — line-based indexing for common term headers and relationships; not full fastobo parity.
  • No OBO write-back in v0.8 — planned for v1.0.
  • Multi-root workspaces — only the first folder is indexed.