Part 7: Slots and inheritance#
Slots and attributes#
Previously we have seen examples of schemas that declare fields/slots using an attributes slot under the relevant class.
In LinkML, “slots” (aka fields) are first-class entities that can be declared outside of classes. The attribute syntax is just a convenient layer on this, but explicit declaration of slots is often preferred for reuse.
(and yes, because LinkML is self-describing, we also talk about metamodel slots)
Let’s see this in action:
personinfo.yaml:
id: https://w3id.org/linkml/examples/personinfo
name: personinfo
prefixes:
linkml: https://w3id.org/linkml/
schema: http://schema.org/
personinfo: https://w3id.org/linkml/examples/personinfo/
ORCID: https://orcid.org/
imports:
- linkml:types
default_range: string
classes:
Person:
class_uri: schema:Person
slots: ## specified as a list
- id
- full_name
- aliases
- phone
- age
id_prefixes:
- ORCID
Container:
attributes:
persons:
multivalued: true
inlined_as_list: true
range: Person
# slots are first-class entities in the metamodel
# declaring them here allows them to be reused elsewhere
slots:
id:
identifier: true
full_name:
required: true
description:
name of the person
slot_uri: schema:name
aliases:
multivalued: true
description:
other names for the person
phone:
pattern: "^[\\d\\(\\)\\-]+$"
slot_uri: schema:telephone
age:
range: integer
minimum_value: 0
maximum_value: 200
The JSON-Schema that is generated should be the same as in the previous example:
gen-json-schema personinfo.yaml
And just as a reminder, we can look at the UML for the schema:
gen-yuml personinfo.yaml
Inheritance#
Now let’s say we want to extend the schema, and we want to include
another class Organization. Organizations may have different
properties from people, but they may also share slots in common - for
example, having a unique identifier and a name
LinkML provides mechanisms for inheritance/polymorphism, we can define a “superclass” called NamedThing, put shared slots in there, and inherit from it.
We also introduce a concept called “mixins” here, which allows for multiple inheritance:
personinfo-with-inheritance.yaml:
id: https://w3id.org/linkml/examples/personinfo
name: personinfo
prefixes:
linkml: https://w3id.org/linkml/
schema: http://schema.org/
personinfo: https://w3id.org/linkml/examples/personinfo/
ORCID: https://orcid.org/
imports:
- linkml:types
default_range: string
classes:
## --
## New parent class
## --
NamedThing:
abstract: true ## should not be instantiated directly
slots:
- id
- full_name
close_mappings:
- schema:Thing
Person:
is_a: NamedThing ## inheritance
mixins:
- HasAliases
class_uri: schema:Person
slots: ## note we only have slots specific to people
- phone
- age
id_prefixes:
- ORCID
Organization:
description: >-
An organization such as a company or university
is_a: NamedThing
class_uri: schema:Organization
mixins:
- HasAliases
slots:
- mission_statement
Container:
tree_root: true
attributes:
persons:
multivalued: true
inlined_as_list: true
range: Person
organizations:
multivalued: true
inlined_as_list: true
range: Organization
## --
## New mixin class
## --
HasAliases:
description: >-
A mixin applied to any class that can have aliases/alternateNames
mixin: true
attributes:
aliases:
multivalued: true
exact_mappings:
- schema:alternateName
slots:
id:
identifier: true
full_name:
required: true
description:
name of the person
slot_uri: schema:name
aliases:
multivalued: true
description:
other names for the person
phone:
pattern: "^[\\d\\(\\)\\-]+$"
slot_uri: schema:telephone
age:
range: integer
minimum_value: 0
maximum_value: 200
mission_statement:
Note that our container object now contains two kinds of lists: people and organization
Here is the schema:
gen-yuml personinfo-with-inheritance.yaml
Renders as:
Let’s take a look at the JSON schema:
gen-json-schema personinfo-with-inheritance.yaml > personinfo-with-inheritance.schema.json
You can see that even though JSON-Schema doesn’t support inheritance, slots from is-a parents and mixins are “rolled down” to their children:
{
"Person": {
"additionalProperties": false,
"description": "",
"properties": {
"age": {
"type": "integer"
},
"aliases": {
"items": {
"type": "string"
},
"type": "array"
},
"full_name": {
"description": "name of the person",
"type": "string"
},
"id": {
"type": "string"
},
"phone": {
"pattern": "^[\\d\\(\\)\\-]+$",
"type": "string"
}
},
"required": [
"id",
"full_name"
],
"title": "Person",
"type": "object"
}
}
Customizing slots in the context of classes: Slot Usage#
LinkML gives you the ability to reuse or inherit slots while customizing them for use in a particular class, using slot_usage
First let’s create a schema where we introduce a new general class Relationship
slot-usage-example.yaml:
id: https://w3id.org/linkml/examples/personinfo
name: personinfo
prefixes:
linkml: https://w3id.org/linkml/
imports:
- linkml:types
default_range: string
classes:
NamedThing:
slots:
- id
- full_name
Person:
is_a: NamedThing
attributes:
has_familial_relationships:
multivalued: true
range: FamilialRelationship
inlined_as_list: true
has_organizational_relationships:
multivalued: true
range: OrganizationalRelationship
inlined_as_list: true
Organization:
is_a: NamedThing
Relationship:
abstract: true
attributes:
duration:
range: integer
related_to:
range: NamedThing
relationship_type:
FamilialRelationship:
is_a: Relationship
slot_usage:
related_to:
range: Person
required: true
relationship_type:
range: FamilialRelationshipType
OrganizationalRelationship:
is_a: Relationship
slot_usage:
related_to:
range: Organization
required: true
relationship_type:
range: OrganizationalRelationshipType
Container:
attributes:
persons:
multivalued: true
inlined_as_list: true
range: Person
organizations:
multivalued: true
inlined_as_list: true
range: Organization
slots:
id:
identifier: true
full_name:
related_to:
relationship_type:
enums:
FamilialRelationshipType:
permissible_values:
SIBLING_OF:
PARENT_OF:
CHILD_OF:
OrganizationalRelationshipType:
permissible_values:
EMPLOYED_BY:
FOUNDED_BY:
LEADER_OF:
MEMBER_OF:
gen-yuml slot-usage-example.yaml
Here we have a fairly generic class Relationship that holds a relationship a person can hold to another entity such as another person or an organization.
there are two subclasses, or for personal relationships (e.g. siblings) and other for person-to-organization relationships. these use the same generic slots (duration, relationship)type, and related_to). However, the latter two are constrained in a class-specific way.
data.yaml:
persons:
- id: ORCID:1234
full_name: Superman
has_organizational_relationships:
- related_to: ROR:1
relationship_type: MEMBER_OF
- id: ORCID:3000
full_name: Jor El
has_familial_relationships:
- related_to: ORCID:1234
relationship_type: PARENT_OF
organizations:
- id: ROR:1
full_name: Justice League
linkml-validate data.yaml -s slot-usage-example.yaml
…