Manage ontology projects

Use ohi add to keep track of the ontologies your project uses. Here we’ll add DCAT 3, which describes data catalogs, and download its dependencies.

Create a project

ohi init city-catalog --default_format owl-turtle
cd city-catalog

This creates a city-catalog folder with your project settings in ohi.yaml. The --default_format owl-turtle option makes OWL in Turtle your preferred format. Leave out that option to use LinkML YAML instead.

Add an ontology

ohi add w3c/dcat@3

You’ll find DCAT at .ohi/w3c/dcat/3/dcat.owl.ttl. Its dependencies, Dublin Core Terms, SKOS and PROV-O, are downloaded into their own folders under .ohi/. ohi records your choice in ohi.yaml and the exact files and checksums in ohi.lock.json.

Run ohi add again to add more ontologies. Leave out @3 to choose the most recently published release. ohi saves that version in ohi.yaml.

Use --format linkml-yaml to choose LinkML YAML for an addition. The CLI reference lists the available formats and defaults.

Restore a project on another machine

Keep ohi.yaml and ohi.lock.json in version control. After cloning the project on another machine, run this from the folder containing those files:

ohi sync

ohi downloads the files recorded in ohi.lock.json into the project’s download folder, .ohi/ by default. Files already present are checked against the saved checksums and reused.

If someone shares only ohi.lock.json, the same command downloads its files into .ohi/. To also create an editable ohi.yaml from that lock, run:

ohi sync --init

ohi creates .ohi/.gitignore to keep downloads out of Git. Edit that file if you want to commit the downloads too. Keep schemas you write yourself outside .ohi/.

Change an ontology’s format

To switch DCAT from Turtle to LinkML YAML, first check which formats DCAT 3 provides:

ohi inspect w3c/dcat@3

Under Files, look for the Format entries. The output includes linkml-yaml, so you can use that value in your project. Open ohi.yaml and change DCAT’s format from owl-turtle to linkml-yaml:

format_version: 1
default_format: owl-turtle
download_dir: .ohi
dependencies:
  - ontology: w3c/dcat@3
    format: linkml-yaml

The format under DCAT applies to that dependency. default_format remains the preference for future add and get commands. You can edit it too if you want future downloads to prefer LinkML.

Apply your change:

ohi sync

This updates ohi.lock.json and downloads DCAT and its dependencies in LinkML YAML. The earlier Turtle files stay in place.

To change versions, follow the same steps with the release you want. For example, run ohi inspect w3c/dcat@2, check its formats, then replace ontology: w3c/dcat@3 with ontology: w3c/dcat@2 in ohi.yaml and run ohi sync. Each version has its own download folder.

Choose another download directory

You can choose a custom download folder when you create a project:

ohi init another-catalog --to ontologies

This saves download_dir: ontologies in ohi.yaml, so downloads go into another-catalog/ontologies/.

Import a downloaded LinkML schema

After downloading the LinkML format, you can import it from a schema next to ohi.yaml. With the default .ohi/ download folder, use:

imports:
  - .ohi/w3c/dcat/3/dcat.linkml

If you chose ontologies/ as your download folder, use ontologies/w3c/dcat/3/dcat.linkml instead. Import paths start from the schema containing them. A schema in models/ would therefore use ../.ohi/w3c/dcat/3/dcat.linkml for the default download folder.

A downloaded schema may import dependencies using other paths or URLs. If ohi LinkML cannot find one, use an import map to point that import to the downloaded file.