Inlining objects

LinkML allows control over whether objects should be inlined or referenced in JSON-style representations using the inlined slot.

Example

For example, given a model with a Organism class that can reference other Organism classes:

classes:
  Organism:
    attributes:
      id:
        identifier: true
      name:
        range: string
      has_subtypes:
        range: Organism
        multivalued: true

for example, the object for “mammals” may be logically related to objects for “primates” and “cats” via the has_subtypes slot. This logical relationship can be serialized in the following different ways:

No inlining, reference by key

schema:

      has_subtypes:
        range: Organism
        multivalued: true
        inlined: false

example data:

- id: NCBITaxon:40674
  name: mammals
  has_subtypes:
    - NCBITaxon:9443
    - NCBITaxon:9682
    - ...
- id: NCBITaxon:9443
  name: primates
  has_subtypes:
    - NCBITaxon:9606
    - ...

Here the range of the has_subtypes slot is a list of strings, where each string is a reference to a separate object

Note that if the range class does not declare an identifier then inlined is always true

Inlining as a list

To force inlining as a list, set inlined_as_list to true

schema:

      has_subtypes:
        range: Organism
        multivalued: true
        inlined: true
        inlined_as_list: true

data:

- id: NCBITaxon:40674
  name: mammals
  has_subtypes:
    - id: NCBITaxon:9443
      name: primates
      has_subtypes:
        - id: NCBITaxon:9606
          name: humans
        - id: NCBITaxon:9682
          ...

Inlining as a dictionary

To force inlining as a list, set inlined_as_list to false

This is a slight variant on inlining as a list - here a dictionary keyed by identifier is provided

Note this is only possible if the range of the slot is a class that has an identifier slot

schema:

      has_subtypes:
        range: Organism
        multivalued: true
        inlined: true
        inlined_as_list: false

data:

- id: NCBITaxon:40674
  name: mammals
  has_subtypes:
    NCBITaxon:9443:
      name: primates
      has_subtypes:
        NCBITaxon:9606:
          name: humans
        NCBITaxon:9682:
          ...

Inlining a single-valued object

Consider a variant of the above schema, with a non-multivalued slot

      has_parent:
        range: Organism
        multivalued: false
        inlined: true

data:

- id: NCBITaxon:9606
  name: human
  has_parent:
    id: NCBITaxon:9443:
    name: primates
    has_parent:
      id: NCBITaxon:40674
      name: mammals

Note on JSON-Schema validation

Currently JSON-Schema validation will fail on any structures inlined as dicts.

Inlining with non-JSON serializations

The concept of inlining only makes sense with JSON-like tree-oriented data serializations:

  • JSON and JSON-LD

  • YAML

  • Programmatic representations such as Python object trees

When serializing data as RDF triples or in a relational database, the value for the slot will always be a reference.

The inlined slot in LinkML corresponds to @embed in JSON-LD

When should inlining be used?

The choice of whether to inline in a JSON representation is application dependent. Inlining can be more convenient for applications that need to traverse an object tree, but inlining can also lead to redundancy in representation and more verbose object payloads.