Part 2: Adding a container object

In part 1 of this tutorial we created a schema for describing people, and showed how we could use this to validate YAML or JSON files with a single person instance.

In practice our data files will rarely be at the level of a single instance. Instead we might have a file that contains a list of people, or a more complex document that contains a variety of different heterogeneous objects.

Example data file

Let’s start with a simple data file that contains more than one instance of person. We choose to structure this as a YAML/JSON dictionary, with an “index slot” called persons:

data.yaml:

persons:
  - id: ORCID:1234
    full_name: Clark Kent
    age: 32
    phone: 555-555-5555
  - id: ORCID:4567
    full_name: Lois Lane
    age: 33

(later on we will see how to express this same thing as a TSV)

Nesting lists of objects

We can describe this data using the following schema.

personinfo.yaml:

id: https://w3id.org/linkml/examples/personinfo
name: personinfo
prefixes:
  linkml: https://w3id.org/linkml/
imports:
  - linkml:types
default_range: string
  
classes:
  Person:
    attributes:
      id:
      full_name:
      aliases:
      phone:
      age:
  Container:
    attributes:
      persons:
        multivalued: true
        inlined_as_list: true
        range: Person

We introduce a class called Container. This doesn’t necessarily reflect a “real world” entity in our domain, it’s just a convenient holder for our data.

Right now it is holding instances of Person but it could hold other kinds of data.

The container has a single attribute/slot called “persons”. This has 3 crucial characteristics:

  • it is multivalued - i.e. it holds a list

  • the range is Person - i.e. the expected values in the data should be people

  • it is inlined - i.e. the values are nested underneath the container

Later on we will explore these in more detail

Validating

We can validate this to make sure we got it right:

linkml-validate -s personinfo.yaml data.yaml 

This should report no errors.

Visualizing

We can use yUML to visualize the schema. The gen-yuml command can generate REST URLs that can be fed into

gen-yuml -f yuml personinfo.yaml 

Outputs:

https://yuml.me/diagram/nofunky;dir:TB/class/[Container]++- persons 0..*>[Person|id:string %3F;full_name:string %3F;aliases:string %3F;phone:string %3F;age:string %3F],[Container]

Which renders as:

img

You can also generate a png directly

gen-yuml -f png personinfo.yaml  > personinfo.png

Exercises

  1. Extend the container object to include dataset-level metadata:

    • description of the dataset

    • name of the dataset

  2. Modify the schema to allow multiple aliases

  3. Modify the test dataset to include multiple aliases for Clark Kent: “Superman” and “Man of Steel”

  4. Validate the data

Further reading

Next

Next we will explore how to add constraints to the schema