Slots#

Slots operate the same way as “fields” in traditional object languages and the same ways as “columns” in spreadsheets and relational databases.

If you have a JSON object that is conformant to a LinkML schema, then the keys for that object must correspond to slots in the schema, that are applicable to that class.

for example, if we have an object instantiating a Person class:

{
  "id": "PERSON001",
  "name": "....",
  "email": "...."
}

then id, email, name should all be valid slots, as in the following schema:

classes:
  Person:
    slots:
      - id
      - name
      - email

If we have tabular data

id

name

email

PERSON0001

…

…

then the same constraints hold.

ranges#

Each slot must have a range - if this is not declared explicitly, then default_range is used.

The range must be one of:

  • A ClassDefinition, when the value of the slot is a complex object

  • A TypeDefinition, when the value of the slot is an atomic object

  • An EnumDefinition, when the value of the slot is a token that represents a vocabulary element

  • A boolean combination of the above

To use a URI or CURIE as a range, create a class with class_uri set to the URI or CURIE and use that class as the range.

Examples:

slots:
  gender:
    slot_uri: schema:gender
    range: GenderType  ## range is an enum
  has_medical_history:
    range: MedicalEvent ## range is a class
    multivalued: true
    inlined_as_list: true
  age_in_years:
    range: integer  ## range is a type
    minimum_value: 0
    maximum_value: 999

slot_usage#

The slot_usage slot can be used to refine the meaning of a slot in the context of a particular class.

For example, imagine a schema with classes Vehicle and VehiclePart, which vehicles can be disassembled into parts:

classes:
  Vehicle:
    slots:
      - make
      - parts
  VehiclePart:
    slots:
      - part_number

slots:
  make:
    range: string
  part_number:
    range: string
  parts:
    range: VehiclePart
    multivalued: true

We can refine the hierarchy:

classes:
  ...
  Car:
    is_a: Vehicle
    slot_usage:
      parts:
        range: CarPart
  Bicycle:
    is_a: Vehicle
    slot_usage:
      parts:
        range: BicyclePart
  CarPart:
    is_a: VehiclePart
  BicyclePart:
    is_a: VehiclePart

In this example, Car and Bicycle are subclasses of Vehicle, and CarPart and BicyclePart are subclasses of VehiclePart. The parts slot is refined to have a range of CarPart for Car and BicyclePart for Bicycle.

Note that LinkML schemas are monotonic. This means it’s not possible to override existing constraints, new constraints are always additive and “layered on”.

In the above example, you can think of a Car having two constraints on the parts slot:

  • one from the Vehicle class, stating that the range is VehiclePart

  • and one from the Car class, stating that the range is CarPart

Rather than the first overriding the second, the two constraints are combined, and the first becomes redundant (because CarPart is a subclass of VehiclePart)

Identifiers#

If a slot is declared as an identifier then it serves as a unique key for members of that class. It can also be used for inlining as a dict in JSON serializations.

slots:
  id:
    identifier: true

the range of an identifier can be any type, but it is a good idea to have these be of type Uriorcurie

A class must not have more than one identifier (asserted or derived). identifier marks the primary identifier.

If you need to mark additional fields as unique, or a collection of slots that when considered as a tuple are unique, use unique_keys (see the constraints section of the docs).

Type designator#

The designates_type slot can be used to indicate the type or category of instances of a class.

slots:
  category:
    designates_type: true

See the type-designators section of the docs for more details.

Cardinality#

In LinkML, slots can be required (mandatory), and they can be singlevalued or multivalued. These are controlled via required and multivalued boolean slots. Additionally, when a slot is multivalued, specific cardinality ranges can be supplied using maximum_cardinality and minimum_cardinality.

Collectively, these metamodel slots define the cardinality of a slot in a data model.

multivalued#

The multivalued indicates that the range of the slot is a list

Example:

slots:
  has_medical_history:
    range: MedicalEvent
    multivalued: true
    inlined_as_list: true

required#

The required slot can be used to define whether a slot is required.

When a slot is declared as required, any class that uses that slot must have a value for that slot.

explicit cardinality ranges#

When a field is multivalued, cardinality can be explicit specified using the following metamodel slots:

Note that specifying exact entails both maximum and minimum, and setting maximum and minimum to be equal entails exact.

Writing cardinality using UML notation#

Cardinality can also be written in UML notation. The following gives an explanation of UML notation and how this maps to LinkML.

  • 1 - Only 1 (required and not multivalued)

  • 0..1 - Zero or one (not required and not multivalued)

  • 1..* - One or more (required and multivalued, with no minimum and maximum cardinality specified)

  • * - Many (not required and multivalued, with no minimum and maximum cardinality specified)

  • n - n (where n>1) (multivalued, with exact_cardinality=n)

  • 0..n - Zero to n (where n>1) (not required and multivalued, with maximum_cardinality=n)

  • 1..n - One to n (where n>1) (required and multivalued, with maximum_cardinality=n)

  • m..n - m to n (where m,n>1) (required and multivalued, with minimum_cardnality=m and maximum_cardinality=n)

inverse#

The inverse slot can be used to specify the inverse predicate of a given predicate slot relationship.

  parent_of:
    is_a: famlially_related_to
    inverse: child_of

For most purposes, the specification of an inverse acts as additional documentation and doesn’t affect programming semantics. However, some frameworks like RDF/OWL allow for the inference of inverses.

default values#

The ifabsent slot can be used to specify a default value for a slot using the syntax shown in the examples below.

Examples:

slots:
  my_string_slot:
    range: string
    ifabsent: string(default value)
  my_int_slot:
    range: integer
    ifabsent: int(42)
  my_float_slot:
    range: float
    ifabsent: float(0.5)
  my_bool_slot:
    range: boolean
    ifabsent: True
  my_date_slot:
    range: date
    ifabsent: date("2020-01-31")
  my_datetime_slot:
    range: datetime
    ifabsent: datetime("2020-01-31T12:00:00Z")
  my_enum_slot:
    range: FamilialRelationshipType
    ifabsent: FamilialRelationshipType(PARENT_OF)

logical characteristics#

Additional logical characteristics can be specified for a slot; these are all boolean: