CLI commands

Run ohi --help for the command overview, or ohi <command> --help for a command’s options.

Command	Purpose
search	Find ontologies by name or topic.
inspect	Show a release’s files and dependencies.
get	Download one ontology file.
init	Create ohi.yaml.
add	Add an ontology to a project and download its dependencies.
sync	Download and verify project ontologies.
lock	Rebuild ohi.lock.json from ohi.yaml.
linkml	Work with local schemas.
version	Print the installed version.

Shared options

Option	Available on	Effect
-h, --help	All commands	Show help.
--json	search, inspect, get, init, add, sync, lock	Write JSON output.
--timeout-ms <number>	search, inspect, get, sync	Positive request timeout in milliseconds. Default 30000.

Ontology references and formats

inspect, get and add accept namespace/name[@version] from ohi.dev, such as w3c/prov-o@2013. Without @version, they select the most recently published release.

get and add use default_format from ohi.yaml, or linkml-yaml if there is no project. If the preferred format is unavailable, they try linkml-yaml. Use --format to require a specific format:

Value	Language	Syntax	Filename suffix
owl-turtle	OWL	Turtle	.owl.ttl
owl-rdfxml	OWL	RDF/XML	.owl
rdfs-turtle	RDFS	Turtle	.rdfs.ttl
linkml-yaml	LinkML	YAML	.linkml.yaml
ossie-yaml	Apache Ossie	YAML	.ossie.yaml

The release must provide exactly one file in the requested format. ohi does not search older releases when a format is unavailable.

search

ohi search <query> [options]

Returns one page of matches from ohi.dev. Quote multiword queries. Use '*' to browse.

ohi search 'energy' --filter-by 'namespace:=saref' --per-page 5

Option	Effect
--page <number>	Page to return, starting at 1. Default 1.
--per-page <number>	Matches per page, from 1 to 250. Default 10.
--filter-by <expression>	Filter matches, for example namespace:=saref.
--sort-by <expression>	Order matches, for example published_at:desc.
--facet-by <fields>	Count values for comma-separated fields, such as namespace.
--max-facet-values <number>	Maximum values per facet, at least 1. Omit to use the search service’s default.
--search-url <url>	Complete search endpoint for another catalog. Requires --query-by.
--query-by <fields>	Comma-separated search fields for that catalog. Requires --search-url.
--color <auto|never>	Color terminal output. Default auto.

Use --page 2 with the same query and options to request the next page. A cutoff warning means the results or counts may be incomplete.

inspect

ohi inspect <namespace/name[@version]> [options]
ohi inspect <release-url> [options]

Shows a release’s metadata, all files, formats and dependency URLs.

ohi inspect w3c/prov-o@2013
ohi inspect https://api.ohi.dev/files/packages/w3c/prov-o/2013/

get

ohi get <namespace/name[@version]> [--format <format>] [options]
ohi get <file-url> [options]

Downloads one ontology file from a reference or Hub file URL.

ohi get w3c/prov-o@2013 --format owl-turtle

Option	Effect
--format <format>	Require a format for an ontology reference. Omit with a file URL.
--to <directory>	Choose a download folder for this command. Relative paths start at the current directory.

Downloads go into download_dir from the current directory’s ohi.yaml, or .ohi/ if there is no project. With the default folder, this example saves .ohi/w3c/prov-o/2013/prov-o.owl.ttl. See Downloaded files for naming and Git settings.

Files are verified using SHA-256 checksums. Matching local files are reused. If a local file has changed, ohi stops and reports its path. Move or delete that file, then retry.

init

ohi init [directory] [--default_format <format>] [--to <directory>] [--json]

Creates ohi.yaml with an empty dependency list. The project directory defaults to the current directory.

ohi init my-project --to ontologies

Option	Effect
--default_format <format>	Set the preferred format. Default linkml-yaml.
--to <directory>	Set the download subfolder. Default .ohi.

The example sets the download folder to my-project/ontologies/. You can edit both settings later in ohi.yaml.

add

ohi add <namespace/name[@version]> [--format <format>] [options]
ohi add <release-url> --artifact <file-url> [options]

Adds the ontology’s version and format to ohi.yaml, updates ohi.lock.json, and downloads the project’s ontologies and dependencies.

ohi add w3c/prov-o@2013 --format owl-turtle

Option	Effect
--format <format>	Require a format for an ontology reference. Omit with a release URL.
--artifact <file-url>	Required with a release URL. Select a file listed by inspect.
--project <directory>	Existing project directory. Default is the current directory.

Downloads use the project’s download_dir. If needed, add creates ohi.yaml with default_format: linkml-yaml and download_dir: .ohi.

For the URL form, use the release and file URLs shown by ohi inspect <reference>.

See Manage ontology projects for the complete workflow.

sync

ohi sync [--project <directory>] [--init] [options]

Downloads missing files and verifies existing files using ohi.lock.json. If you changed the dependencies in ohi.yaml, or there is no lock yet, sync updates the lock before downloading. If a local file has changed, move or delete the reported file, then rerun ohi sync.

ohi sync --project ./my-project

Option	Effect
--project <directory>	Directory containing ohi.yaml, ohi.lock.json, or both. Default is the current directory.
--init	Create ohi.yaml from a shared lock if it is missing.
--color <auto|never>	Color terminal output. Default auto.

Downloads use download_dir from ohi.yaml. With only a lockfile, they go into .ohi/. A new ohi.yaml keeps the selected versions and formats, with default_format: linkml-yaml and download_dir: .ohi. If neither project file exists, start with ohi init or ohi add.

lock

ohi lock [--project <directory>] [--json]

Rebuilds ohi.lock.json using the versions and formats in ohi.yaml, without downloading files.

ohi lock --project ./my-project

--project defaults to the current directory.

linkml

Runs LinkML schema validation, conversion and generation commands. Use the complete command’s help for its arguments and options:

ohi linkml --help
ohi linkml validate --help
ohi linkml to json-schema --help

version

ohi version

Prints the installed ohi and component versions. --format <terminal|json> selects the output format. Default is terminal.