How-to Guides

Some of these guides are works in progress

Contents:

• LinkML Project Cookiecutter
  • LinkML Project Cookiecutter Quickstart
  • Use cruft to create your brand new LinkML project:
  • Build your LinkML project
• How to run a collaborative data modeling project
  • Sources
  • Principles
  • Open Science Principles
  • Example Governance and Community Documents
• How to recognize and work with different structural forms
  • Introduction
  • Structural Forms
• Using yq for querying and manipulating schemas
  • top level lookups
  • all class names
  • classes with their is-a parents
  • setting top level slots
  • lookup a class by name
  • Setting the is_a value of a class:
  • prefixes
• Using JSON-LD
  • About JSON-LD
  • JSON-LD Example
  • Coordinating JSON-Schema and JSON-LD Contexts
  • LinkML and JSON-LD
• How to model quantities and measurements
  • Central Example
  • Requirements
  • Core schema
  • Patterns and Anti-patterns
  • Case Studies
  • Further Reading
• Porting LinkML tools to other programming languages
  • Preamble
  • Introduction
  • Data class generators
  • Definitions
  • Overview of Python Framework
  • How to Port to your language of choice
  • Summary
• Multidimensional Arrays
  • Background
  • Alternatives: Wide table representation
  • N-Dimensional Arrays in LinkML
  • Further discussion
• How to make a property graph schema
  • What is a property graph?
  • First attempt: A simple graph projection
  • Second attempt: Standard PG Pattern: Node and Edge classes
  • See Also
• How to Generate AI prompts
  • Introduction Preamble
  • Objective
  • Generating prompts from LinkML schemas
  • Further exploration: Text extraction with OntoGPT and SPIRES
  • Other use cases
  • Questions
• Deprecating elements while maintaining PURLs and other URIs
  • First release cycle:
  • Second release cycle:
  • Generating deprecated elements in online documentation
• Using ontology terms as values in data
  • Motivating Example: associations to ontology terms.
  • Representing the ontology hierarchy as data
  • Ontology class hierarchies and LinkML class hierarchies need not be mirrored
  • When should hierarchies be mirrored?