Models

A LinkML model describes the structure of your data. Your data can be expressed as JSON or YAML files (the default form for LinkML), or as CSVs, or as a relational database, or even a triplestore or graph database.

LinkML models are authored as YAML files. These files can be understood as data files that instantiate SchemaDefinitions in the LinkML metamodel.

To illustrate we will use the example PersonSchema

Model metadata and directives

A LinkML model/schema may have various pieces of metadata associated with it, for example:

id: https://w3id.org/linkml/examples/personinfo
name: personinfo
description: |-
  Information about people, based on [schema.org](http://schema.org)
license: https://creativecommons.org/publicdomain/zero/1.0/
default_curi_maps:
  - semweb_context
imports:
  - linkml:types
prefixes:
  personinfo: https://w3id.org/linkml/examples/personinfo/
  linkml: https://w3id.org/linkml/
  schema: http://schema.org/
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  prov: http://www.w3.org/ns/prov#
default_prefix: personinfo
default_range: string
...
  • names, identifiers, and metadata

    • id – the unique identifier for the schema, as a IRI

    • name – the schema name. Use only alphanumeric characters, underscores, and dashes

    • description – a summary of the schema. Can include markdown formatting

    • license – CC0 recommended

  • modules

  • prefix management

  • other

Classes

Classes provide templates for organizing data. Data objects should instantiate classes in the schema. Each class has a set of slots (aka fields, attributes) that are applicable to it.

Classes are defined in a classes block at the top level of your YAML:

classes:
  Person:
    is_a: NamedThing
    description: >-
      A person (alive, dead, undead, or fictional).
    class_uri: schema:Person
    mixins:
      - HasAliases
    slots:
      - primary_email
      - birth_date
      - age_in_years
      - gender
      - has_employment_history
      - has_familial_relationships
      - has_medical_history

See ClassDefinition for a full list of allowed slots

Note that because LinkML is described in LinkML, your schema is an instantiation of the LinkML metamodel, and schema elements have a list of allowed slots. So for example, is_a, description, and slots are all slots that are applicable to instances of ClassDefinitions. This is a little meta at first but you get used to it!

Slots

Slots (aka attributes, fields, columns, properties) can be associated with classes to specify what fields instances of that class can have

For example, in the schema above, instances of Person classes can have values for primary email, birthdate, etc.

In LinkML slots are “first class” and are defined independently of classes, and a slot can be used in any number of classes.

Slots are defined in a slots block at the top level of your YAML:

slots:
  id:
    identifier: true
    slot_uri: schema:identifier
  name:
    slot_uri: schema:name
  gender:
    slot_uri: schema:gender
    range: gender_enum
  age_in_years:
    range: integer
    minimum_value: 0
    maximum_value: 999
  has_employment_history:
    range: EmploymentEvent
    multivalued: true
    inlined_as_list: true
  current_address:
    range: Address
    

See SlotDefinition for a full list of allowed slots

The Attribute slot

As a convenience feature, you can specify slot definitions directly within a class using the attributes slot:

classes:
  Person:
    is_a: NamedThing
    description: >-
      A person (alive, dead, undead, or fictional).
    class_uri: schema:Person
    mixins:
      - HasAliases
    attributes:
      gender:
        slot_uri: schema:gender
        range: gender_enum
      age_in_years:
        range: integer
        minimum_value: 0
        maximum_value: 999

Slot Usage

Sometimes you may wish to use a generic slot across multiple classes, but refine its usage for particular subclasses.

For example, imagine a schema with a generic “Relationship” class:

  Relationship:
    slots:
      - started_at_time
      - ended_at_time
      - related_to
      - type

with subtypes such as FamilialRelationship, BusinessRelationship, etc

we can use slot_usage to constrain the meaning of more generic slots such as type and related to:

  FamilialRelationship:
    is_a: Relationship
    slot_usage:
      type:
        range: FamilialRelationshipType
        required: true
      related to:
        range: Person
        required: true

Types

See TypeDefinition in the metamodel.

Types in LinkML are scalar data values such as strings, integers, floats, and so on. LinkML comes with its own set of types, and these can be extended.

TODO: example

Enums

enums:
  FamilialRelationshipType:
    permissible_values:
      SIBLING_OF:
      PARENT_OF:
      CHILD_OF:

Subsets

TODO: example