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OBO authoring (v0.13+)

Edit OBO Format 1.4 (.obo) files in VS Code via the Entity Inspector and strixonomy patch. Requires Strixonomy v0.13.0+ or strixonomy-cli 0.13.0+.

Related: OBO workflows · Patch reference · What ships today

Quick start

  1. Open a workspace with .obo files (bundled LSP works in Restricted Mode).
  2. Select a term in the explorer or open a .obo file.
  3. Open the Entity Inspector — edit name, synonyms, definition, is_a parent, namespace, or deprecated flag.
  4. Preview then Apply (same flow as Turtle).

Inspector vs raw file

Approach When to use
Entity Inspector Term metadata, parents, synonyms — guided forms
Direct .obo edit Bulk edits, version control diffs, ROBOT pipelines
strixonomy patch CI, scripts, LSP integrators

RDF/XML and OWL/XML also support write-back (v0.21+, semantic re-serialize). JSON-LD remains read-only in the inspector. See Supported formats.

Patch operations

OBO patches use term_id (e.g. GO:0008150), not entity_iri. Ops are applied by strixonomy-obo.

op Purpose
set_name Replace term name
add_synonym / remove_synonym Synonyms with scope (EXACT, RELATED, …)
add_def / remove_def Definition text
add_xref / remove_xref Database cross-references
set_namespace Term namespace
set_deprecated is_obsolete flag
add_is_a / remove_is_a Parent terms

Full schema: Patch reference — OBO operations.

CLI example

strixonomy patch ./terms.obo --preview '[
  {"op": "set_name", "term_id": "EX:001", "value": "example class"},
  {"op": "add_is_a", "term_id": "EX:001", "parent_id": "EX:000"}
]'
strixonomy patch ./terms.obo patches.json

Copy-paste samples: examples/patches.md

LSP

Method: strixonomy/applyAxiomPatch with document_uri pointing at a .obo file. Same envelope as Turtle; ops use term_id. See LSP API.

Limits (v0.12)

  • No Manchester or OWL axiom editing on OBO files — use Turtle/OWL for complex logical axioms.
  • Logical definitions and some xref encodings may require Protégé or ROBOT for full parity.
  • Mixed workspaces (.obo + .ttl) index together; write-back applies per file format.

Troubleshooting

Problem Fix
Inspector read-only Confirm v0.12+; entity must be in an indexed .obo file
unsupported format Patch target must be .obo with OBO ops
Term not found Check term_id matches the file (e.g. GO:0008150)

See Troubleshooting and OBO workflows.