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>
Required option

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.

Arguments

SCHEMA
Required argument

Examples

Example 1: Trim Biolink Schema 

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