Command Line Interface

bioregistry automatically installs the command bioregistry. See bioregistry --help for usage details.

bioregistry

Run the Bioregistry CLI.

Usage

bioregistry [OPTIONS] COMMAND [ARGS]...

Options

--version: Show the version and exit.

align

Align all external registries.

Usage

bioregistry align [OPTIONS]

Options

--skip-fairsharing

--skip-re3data

--skip-bioportal

--skip-agroportal

--skip-slow

--no-force

compare

Compare the registries.

Usage

bioregistry compare [OPTIONS]

curate

Curation workflows.

Usage

bioregistry curate [OPTIONS] COMMAND [ARGS]...

linkml

Import from LinkML.

Usage

bioregistry curate linkml [OPTIONS] URL

Arguments

URL: Required argument

export

Export as SSSOM, RDF, TSV, and other formats.

Usage

bioregistry export [OPTIONS]

generate-schema

Dump the JSON schemata.

Usage

bioregistry generate-schema [OPTIONS]

lint

Run the lint commands.

Usage

bioregistry lint [OPTIONS]

update

Update the Bioregistry.

Usage

bioregistry update [OPTIONS]

validate

Validate data with the Bioregistry.

Usage

bioregistry validate [OPTIONS] COMMAND [ARGS]...

jsonld

Validate a JSON-LD file.

Usage

bioregistry validate jsonld [OPTIONS] LOCATION

Options

--relax

--context <context>: The Bioregistry context, e.g., obo. If none given, uses the default Bioregistry context.

--use-preferred: If true, use preferred prefixes instead of normalized ones. If a context is given, this is disregarded.

--tablefmt <tablefmt>

The table format to use with the tabulate package.

Options:: github | rst

Arguments

LOCATION: Required argument

linkml

Validate prefixes in a LinkMK YAML configuration.

Usage

bioregistry validate linkml [OPTIONS] URL

Options

--relax

--context <context>: The Bioregistry context, e.g., obo. If none given, uses the default Bioregistry context.

--use-preferred: If true, use preferred prefixes instead of normalized ones. If a context is given, this is disregarded.

--tablefmt <tablefmt>

The table format to use with the tabulate package.

Options:: github | rst

Arguments

URL: Required argument

ttl

Validate prefixes in a Turtle file (either remove or local).

For example, you can validate an old version of the chemotion knowledge graph. It has the following prefixes:

@prefix nfdicore: <https://nfdi.fiz-karlsruhe.de/ontology/> . @prefix ns1: <http://purls.helmholtz-metadaten.de/mwo/> . @prefix ns2: <http://purl.obolibrary.org/obo/chebi/> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

The Bioregistry will error on ns1 and ns2 since they’re not standard prefixes. Run it like this:

$ bioregistry validate ttl https://github.com/ISE-FIZKarlsruhe/chemotion-kg/raw/4cb5c24af/processing/output_bfo_compliant.ttl

See follow-up discussion on improving the chemotion-kg using this feedback in https://github.com/ISE-FIZKarlsruhe/chemotion-kg/issues/2

Usage

bioregistry validate ttl [OPTIONS] LOCATION

Options

--relax

--context <context>: The Bioregistry context, e.g., obo. If none given, uses the default Bioregistry context.

--use-preferred: If true, use preferred prefixes instead of normalized ones. If a context is given, this is disregarded.

--tablefmt <tablefmt>

The table format to use with the tabulate package.

Options:: github | rst

Arguments

LOCATION: Required argument

virtuoso

Validate prefixes in a Virtuoso SPARQL server.

Usage

bioregistry validate virtuoso [OPTIONS] URL

Options

--relax

--context <context>: The Bioregistry context, e.g., obo. If none given, uses the default Bioregistry context.

--use-preferred: If true, use preferred prefixes instead of normalized ones. If a context is given, this is disregarded.

--tablefmt <tablefmt>

The table format to use with the tabulate package.

Options:: github | rst

Arguments

URL: Required argument

web

Run the web application.

Usage

bioregistry web [OPTIONS]

Options

--host <host>

The host to serve to

Default:: '0.0.0.0'

--port <port>

The port to serve on

Default:: 5000

--with-gunicorn: Use gunicorn instead of flask dev server

--workers <workers>: Number of workers

-v, --verbose: Enable verbose mode. More -v’s means more verbose.

--registry <registry>: Path to a local registry file

--metaregistry <metaregistry>: Path to a local metaregistry file

--collections <collections>: Path to a local collections file

--contexts <contexts>: Path to a local contexts file

--config <config>: Path to a configuration file

--analytics

--base-url <base_url>

Base URL for app

Default:: 'https://bioregistry.io'

--tab: If passed, automatically opens a web browser