Work Instructions

Create a new schema from scratch

  1. Open the main menu
  2. Click on the New button
  3. Click on Store in: Web Browser Storage

Import an existing schema

  1. Open the main menu
  2. Click on the Import button
  3. Choose a file in your file system, or paste a valid schema in the text area
  4. Click on the Import button at the bottom of the panel

Importing a schema doesn’t override the current schema.

Schemalink validates the schema you import, and return validation errors. A non-valid schema can still be imported, but might lead to unexpected results.

Edit schema properties

  1. Make sure the inspector panel is visible by clicking on any empty space in the canvas.

  2. Within the inspector panel, edit:

    • The schema description
    • The schema license

Change the schema name

  1. Click on the schema name
  2. Edit the name
  3. Click on Save

Add a class

  1. Make sure the inspector panel is visible by clicking on any empty space in the canvas.
  2. Click on the Add Class button in the general inspector
  3. Specify a class name

Classes without a name as well as classes with a non-unique name won’t be included in any LinkML export. This also applies relationships that involve those classes.

Add a relationship

  1. Hover upon the perimeter of a class, until a dark blue circle appears.
  2. Drag the circle to another existing class, or to an empty space to create a new class at the same time.

Edit a class

  1. Select a class or a set of classes (cmd+click in Mac, ctrl+click in Linux and Windows).

  2. Using the form in the detail inspector, edit:

    • The class description
    • The class name
    • The class ontologies and examples - details below
    • The class attributes - details below

Only some options will be available if more than one class is selected.

Edit a relationship

  1. Select a relationship or a set of relationships (cmd+click in Mac, ctrl+click in Linux and Windows).

  2. Using the form in the detail inspector, edit:

    • The relationship description
    • The relationship name
    • The type of relationship (association or inheritance)
    • The relationship cardinality
      • Expand the cardinality dropdown menu and select a predefined cardinality or Custom.
      • If Custom is selected, specify minimum and maximum cardinality for both the source and the target.
    • The relationship ontologies and examples - details below
    • The relationship attributes - details below

When Custom is selected, if the minimum cardinality is greater or equal than the maximum cardinality, neither of them will be included in any LinkML export.

Only some options will be available if more than one relationship is selected.

Annotate classes and elationships with ontologies and provide examples for instances

  1. Click on a single class or relationship.
  2. In the inspector, expand the ontologies dropdown menu and select those that are relevant.
  3. In the inspector, expand the examples dropdown menu and select those that are relevant.

By default, the dropdown will show ten examples, randomly selected from selected ontologies’ terms.

If no ontology is selected, the examples dropdown will be empty.

You can add new examples by just typing them in the input field.

Ontologies and examples are fetched from a EBI’s Ontology Look-up Service. Every time Schemalink is loaded or the set of ontologies for annotating a class is changed, you have to wait for the dropdown menu to be enabled.

Add and edit attributes for classes and relationships

  1. Select a class, a relationship, or a set taht includes classes and relationships
  2. In the inspector, click on the + Attribute button
  3. Provide a name for the attribute

  4. Optional: click on the edit panel and add:

    • The attribute description
    • The attribute range (i.e. the type of that attribute)
    • The attribute collection type, if any
    • Whether the attribute is required
    • Whether the attribute is the identifier of its class

Export the schema

  1. Click on the download/export button
  2. Choose the format you want to export the schema to, by switching to the corresponding tab
  3. Check the preview to make sure the export is correct
  4. Click on Download

Change the graphical style of the schema

Click on Style in the inspector panel to expand the style menu. <!– 2. Use the form to change a variety of style options, such as:

The general inspector and the detail inspector offer different styling options. Namely, the general inspector allows to perform global changes, while the detail inspector allows to perform changes on a per-entity basis. –>