owl2vault

Generate a LinkML schema, an Obsidian-ready Markdown vault and MkDocs from an OWL ontology.

Quick start

• On Ubuntu LTS with a managed Python, avoid system-wide pip (PEP 668). Use a venv:
  • sudo apt-get install -y python3-venv python3-pip
  • python3 -m venv .venv
  • source .venv/bin/activate
  • pip install -e .
  • Run owl2vault ... while the venv is active (or use .venv/bin/owl2vault).

Quick start (Docsify + Hugo)

• Generate Docsify output and serve it locally:
  • owl2vault -i path/to/schema.owl --docsify output/docsify
  • cd output/docsify && python -m http.server 8000
  • Site serves at http://127.0.0.1:8000 (change port by replacing 8000).
• Generate Hugo output and serve it locally (requires Hugo installed):
  • owl2vault -i path/to/schema.owl --hugo output/hugo
  • cd output/hugo && hugo server
  • Site serves at http://127.0.0.1:1313 by default (change port with hugo server -p 9000).

CLI options

• -i / --input: path to the OWL file to load.
• --url: URL to download an OWL file to use as input.
• --linkml: path to write the generated LinkML YAML.
• --vault: directory to write the Obsidian vault (creates Classes/, Enums/, Object_Properties/, Data_Properties/, Annotation_Properties/, 00-Index/).
• --mkdocs: directory to write a MkDocs project (mkdocs.yml + docs/ with markdown).
• --docsify: directory to write a Docsify project (index.html + docs/ with markdown).
• --hugo: directory to write a Hugo project (config.toml + content/ with markdown).
• --log-level: ERROR|WARNING|INFO|DEBUG (default: INFO).

Usage examples

• Generate LinkML YAML only:
  • owl2vault -i path/to/schema.owl --linkml output/schema.yaml
• Generate an Obsidian vault only:
  • owl2vault -i path/to/schema.owl --vault output/vault
• Generate MkDocs docs only:
  • owl2vault -i path/to/schema.owl --mkdocs output/mkdocs
• Generate Docsify docs only:
  • owl2vault -i path/to/schema.owl --docsify output/docsify
• Generate a Hugo site only:
  • owl2vault -i path/to/schema.owl --hugo output/hugo
• Generate both MkDocs and Docsify in one run:
  • owl2vault -i path/to/schema.owl --mkdocs output/mkdocs --docsify output/docsify
• Generate MkDocs, Docsify, and Hugo together:
  • owl2vault -i path/to/schema.owl --mkdocs output/mkdocs --docsify output/docsify --hugo output/hugo
• Pull OWL from a URL then generate everything:
  • owl2vault --url https://ekgf.github.io/dprod/dprod.ttl --linkml output/schema.yaml --vault output/vault --mkdocs output/mkdocs
• Build and serve MkDocs docs after generation:
  • cd output/mkdocs && mkdocs build && mkdocs serve (serve at http://127.0.0.1:8000 by default)
• MkDocs dependencies for theming/graphs:
  • pip install mkdocs-material
  • pip install "mkdocs-material[imaging]"
  • pip install mkdocs-network-graph-plugin
• Do both with verbose logging:
  • owl2vault -i path/to/schema.owl --linkml output/schema.yaml --vault output/vault --log-level DEBUG
• Generate LinkML YAML, then build markdown docs with linkml’s generator:
  • owl2vault -i path/to/schema.owl --linkml output/schema.yaml
  • gen-doc --format markdown --output docs/ output/schema.yaml

Outputs

• LinkML: YAML schema with classes, slots, enums, and properties.
• Obsidian vault: per-entity markdown notes under Classes/, Enums/, Object_Properties/, Data_Properties/, Annotation_Properties/, Datatypes/, Individuals/, plus 00-Index/Index.md linking everything. Notes use stable IRI-derived IDs and headings use labels when available (IRI fallback). Class sections list “Properties” (not “Slots”), and annotation predicates/IRI-valued annotations display resolved labels where available.
• MkDocs: mkdocs.yml (uses the material theme with graph, search, and optimize plugins) plus docs/ with markdown grouped into classes/, enums/, object_properties/, data_properties/, annotation_properties/, datatypes/, individuals/, and an index.md linking everything. Use mkdocs build to generate a site. Annotation predicates/IRI-valued annotations are rendered with their labels when present.
• Docsify: index.html plus docs/ with markdown grouped into classes/, enums/, object_properties/, data_properties/, annotation_properties/, datatypes/, individuals/, and a README.md home page. _sidebar.md is generated from the same nav structure.
• Hugo: config.toml plus content/ with markdown grouped into classes/, enums/, object_properties/, data_properties/, annotation_properties/, datatypes/, individuals/, and a _index.md home page.

Version

• Current version: 0.1.8