Work Instructions
Create a new schema from scratch
- Open the main menu
- Click on the ``New’’ button
- Click on
Store in: Web Browser Storage
Import an existing schema
- Open the main menu
- Click on the
Import
button - Choose a file in your file system, or paste a valid schema in the text area
- Click on the
Import
button at the bottom of the panel
Importing a schema does not override the current schema. Schemas will be merged.
Schemalink validates the imported schema and points out validation errors. A non-valid schema can still be imported but might lead to unexpected results.
Edit schema properties
- Make sure the
inspector
panel is visible by clicking on any empty space in the canvas. -
Within the
inspector
panel, edit:- The schema
description
- The schema
license
- The schema
Change the schema name
- Click on the schema
name
- Edit the name
- Click on Save
Add a class
- Make sure the
inspector
panel is visible by clicking on any empty space in the canvas. - Click on the
Add Class
button in theinspector
panel - Specify a class
name
Classes without a name as well as classes with a non-unique name will not be included in any LinkML export. This also applies to relationships that involve those classes.
Add a relationship
- Hover upon the perimeter of a class, until a dark blue circle appears
- Drag the circle to another existing class, or to an empty space to create a new class at the same time
Edit a class
- Select a class or a set of classes (
cmd+click
in Mac,ctrl+click
in Linux and Windows) -
Using the form in the detail inspector, edit:
- The class
description
- The class
name
- The class
ontologies
andexamples
- details below - The class
attributes
- details below
- The class
Only some options will be available if more than one class is selected.
Edit a relationship
- Select a relationship or a set of relationships (cmd+click in Mac, ctrl+click in Linux and Windows)
-
Using the form in the detail inspector, edit:
- The relationship
description
- The relationship
name
- The
type
of relationship (association
orinheritance
) - The relationship
cardinality
- Expand the
cardinality
dropdown menu and select a predefined cardinality orCustom
. - If
Custom
is selected, specifyminimum
andmaximum cardinality
for both the source and the target.
- Expand the
- The relationship
ontologies
andexamples
- details below - The relationship
attributes
- details below
- The relationship
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 relationships with ontologies and provide examples for instances
- Click on a single class or relationship
- In the
inspector
, expand theontologies
dropdown menu and select those that are relevant - In the
inspector
, expand theexamples
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 an EBI Ontology 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
- Select a class, a relationship, or a set that includes classes and relationships
- In the
inspector
, click on the+ Attribute
button - Provide a
name
for the attribute -
Optional: click on the edit panel and add:
- The attribute
description
- The attribute
range
(i.e. thetype
of that attribute) - The attribute
collection type
, if any - Whether the attribute is
required
- Whether the attribute is the
identifier
of its class
- The attribute
Export the schema
- Click on the
download/export
button - Choose the format you want to export the schema to, by switching to the corresponding tab
- Check the preview to make sure the export is correct
- Click on the
Download
button
Change the graphical style of the schema
Click on Style
in the inspector
panel to expand the style menu. <!–
- 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. –>