# Inlining objects

LinkML allows control over whether objects should be *inlined* or *referenced* in JSON-style representations using the [inlined](https://w3id.org/linkml/inlined) slot.

## Example

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

```yaml
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:

```yaml
      has_subtypes:
        range: Organism
        multivalued: true
        inlined: false
```

example data:

```yaml
- 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](https://w3id.org/linkml/identifier) then `inlined` is always true

## Inlining as a list

To force inlining as a list, set [inlined_as_list](https://w3id.org/linkml/inlined_as_list) to `true`

schema:

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

data:

```yaml
- 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 dictionary, set [inlined_as_list](https://w3id.org/linkml/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:

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

data:


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

Note that in the above the `id` field is *not* included in the actual
organism object, as it is acting as a key for that object, it doesn't 
need to be included. However, it is still legal to include it,
like this:

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

## Inlining a single-valued object

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

```yaml
      has_parent:
        range: Organism
        multivalued: false
        inlined: true
```

data:


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

```

## Inlining as simple dictionaries

If a collection of objects is inlined as a dict, and the objects have a "primary" value, then
a more compact simple key-value pair inlining can be used.

One example of this is [prefixes](https://w3id.org/linkml/prefixes) in the LinkML metamodel. This is an
inlined collection of [Prefix](https://w3id.org/linkml/Prefix) classes which are essentially tuples of
a key (the prefix itself, e.g. `dcterms`) and a value (the expansion, e.g. `http://purl.org/dc/terms/`).

These can be serialized in the standard compact form like this:

```yaml
prefixes:
  dcterms:
    prefix_reference: http://purl.org/dc/terms/
  ...
```

However, the canonical encoding is the more compact SimpleDict form:

```yaml
prefixes:
  dcterms: http://purl.org/dc/terms/
```

The procedure for determining whether a SimpleDict serialization can be used
on a collection of classes is as follows:

1. There must be a key or identifier slot (this is true for all slots inlined as dict)
2. One of the following must hold of the set of remaining slots:
    - There is exactly one additional non-key slot (this forms the "primary" value)
    - If there are multiple candidates for the primary value, if exactly one is `required`, it is used.

## 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.