LinkML Schemas

This introduces the key parts of LinkML that you need to know to create a schema in order to model your data.

Note that the formal specification for LinkML can be found at https://w3id.org/linkml/specification. This formal specification is aimed at implementers and not users. General users of LinkML should use the guide below.

Contents:

• Models
  • Model-level metadata and directives
  • Classes
  • Slots
  • Types
  • Enums
  • Subsets
  • Metamodel
• Schema Element Metadata
  • Providing descriptions
  • Providing aliases
  • Structured aliases
  • Deprecating elements
  • Specifying units
  • Other metadata slots
• Inheritance
  • Linking classes and slots with is_a
  • Abstract classes and slots
  • Mixin classes and slots
  • Materializing inherited slots
• Slots
  • ranges
  • slot_usage
  • Identifiers
  • Type designator
  • Cardinality
  • inverse
  • default values
  • logical characteristics
• Arrays
  • Types
  • NDArrays
  • Generators
  • See Also
  • References
• URIs and Mappings
  • background: URIs, IRIs, and CURIEs
  • URI Prefixes
  • class uri and slot uri
  • Enumerations and the meaning slot
  • Relationship to ISO-11179-3
  • mappings
  • id_prefixes
  • See Also
• Semantic Enumerations
  • Basic Enums
  • Mapping Permissible Values to Ontologies
  • Working with Enums in Python
  • Dynamic Enums
  • Tooling to support dynamic enums
• Inlining objects
  • Example
  • No inlining, reference by key
  • Inlining as a list
  • Inlining as a dictionary
  • Inlining a single-valued object
  • Inlining as simple dictionaries
  • Inlining with non-JSON serializations
  • When should inlining be used?
• Adding constraints and rules
  • Unique Key
  • String serialization
  • Patterns
  • Structured patterns
  • Minimum and Maximum values
  • Expressions and other advanced features
• Type designators
• Subsets
• Imports
  • Importing external schemas
  • Local imports
  • Making merged files for distribution
• Advanced features
  • LinkML Any type
  • Boolean constraints
  • Rules
  • Defining slots
  • equals_expression
  • URI or CURIE as a range
• Mapping schemas to other frameworks
• Schema Linter
  • Introduction
  • Configuration
  • Rules
  • Reports
  • Exit Codes
  • API Docs
• Derived models
  • Asserted vs Derived Models/Schemas
  • Materializing a derived model
  • Programmatically inferring models
  • Specification
• Annotations
  • Background
  • Adding your own annotations
  • Annotation validation
  • Validation of annotations
  • Other uses of instantiates
• The metamodel
  • Metamodel Versioning scheme
  • Release Candidates
  • Metamodel Release Notes
• Expression Language
  • Syntax
  • Limitations
  • Examples

See also

Programmatic example in a Jupyter Notebook