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 |
|
---|---|---|
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
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 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
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 constraits section of the docs).
Slot cardinality#
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.
recommended#
The recommended slot can be used to define whether a slot is recommended.
If data is missing a recommended slot, it is still considered valid. However, validators may choose to issue warnings.
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
logical characteristics#
Additional logical characteristics can be specified for a slot; these are all boolean: