LinkML Schema Trimmer

Overview

Generate a trimmed version of a LinkML schema by only including a specific subset of classes, slots, and enums.

Command Line

bkbit linkml-trimmer

$ bkbit linkml-trimmer [OPTIONS] SCHEMA

Options

-c, --classes <classes>

List of ‘classes’ to include in the trimmed schema.

Note: Classes must be separated by commas and enclosed in quotes.

-s, --slots <slots>

List of ‘slots’ to include in the trimmed schema.

Note: Slots must be separated by commas and enclosed in quotes.

-e, --enums <enums>

List of ‘enums’ to include in the trimmed schema.

Note: Enums must be separated by commas and enclosed in quotes.

-i, --schema_id <schema_id>

Updated schema id for trimmed schema.

-n, --schema_name <schema_name>

Updated schema name for trimmed schema.

-t, --schema_title <schema_title>

Updated schema title for trimmed schema.

-v, --schema_version <schema_version>

Updated schema version for trimmed schema.

Arguments

SCHEMA

Type: str | Path | SchemaDefinition

Examples

Example 1: Trim Schema (Local File):

$ bkbit linkml-trimmer --classes "gene, genome, organism taxon, thing with taxon, material sample, procedure, entity, activity, named thing, relative frequency analysis result" biolink-model.yaml > bican-biolink.yaml

Example 2: Trim Schema (URL):

$ bkbit linkml-trimmer --classes "gene, genome, organism taxon, thing with taxon, material sample, procedure, entity, activity, named thing, relative frequency analysis result" "https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/biolink-model.yaml" > bican-biolink.yaml