OBO workflows¶

Strixonomy v0.12.0 indexes OBO Format (.obo) files via fastobo and exposes obo_id in the catalog and SQL virtual tables. OBO write-back ships in v0.12 via the strixonomy-obo crate — Entity Inspector forms and strixonomy patch for .obo files.

Canonical capability matrix: What ships today.

Prerequisites¶

• Strixonomy v0.12.0+ or strixonomy-cli 0.12.0+
• 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 Strixonomy: 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).

Edit in VS Code (v0.12+)¶

1. Open an OBO term in the Entity Inspector.
2. Edit name, synonym, definition, is_a parent, namespace, or deprecated flag.
3. Use Preview then Apply (same preview-before-apply flow as Turtle).

Patch ops use term_id (not entity_iri). See patch reference and migration/v0.12.md.

CLI patch¶

strixonomy patch path/to/terms.obo --preview '[{"op":"set_name","term_id":"EX:001","value":"renamed"}]'

Query obo_id from SQL¶

strixonomy 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¶

Example workspace¶

Repository example: examples/obo-workflow/

git clone https://github.com/eddiethedean/strixonomy.git
cd strixonomy
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 strixonomy robot validate and CI recipes.

Limitations¶

• OBO patch scope — v0.12 covers common term headers (name, synonyms, def, xref, is_a, namespace, deprecated); not every OBO construct.
• Multi-root workspaces — all folders indexed since v0.10; ensure each root contains ontology files

Related¶

• ROBOT interop
• Authoring
• FAQ
• v0.12 migration