Curator View

Entities View

Entity Link-outs

Within the curator view, you can search for additional information about text mentions (already annotated or not) in Web-accessible databases, accounting for unfamiliar terminology and confirming some classifications.

Text Annotation Link Outs

To access the external links, select a term in the text and choose the option External Links in the popup menu.

Then, a list with links to external databases appears and you should select the appropriate link to the term context. New tabs are opened in your browser with the respective URLs: one with the selected text and, if external IDs have been associated with the selected term, others directly pointing to External IDs associated to the term in eternal databases.

The External Links mentioned above can be edited in the GUI for managing external IDs and linkouts

Tree Entities Link Outs

In the tree with classes (right side panel in the Curator View) the user can search entities annotated divided by classes an grouped in a tree. Some annotated entities have information on DatabaseID, Synonyms, Annotated Synonyms ad External Ids. You can click in an External Id to open a direct link-out for the external source and respective record.

Entity Management

Add Entity

To annotate a new term, select the term and a pop-up window will appear with the possible options, i.e. biological classes. The Add Annotation option must be chosen and the intended class selected. If the selected term is already annotated, it can't be annotated again.

You can annotate an entity with a new class selecting the option 'new class' . In this case, a window is launched to add a new class.

• Notes
  • If a Lookup Table is enabled the changes are propagated to this lookup table. (The changes will be made in the underlying database supporting the lookup table and can therefore be used to annotate other documents in the future.)
  • If the All Text option is selected, all annotations for instances of this term are added; otherwise just the selected annotation is added.
  • Selecting All text option you can select case sensitive or not in case sensitive button.

Edit Entity

Within the curator view, it is possible to correct an annotation. This correction can be done in the lexical form of the term or changing the class that the term is assigned to. To do so, select the term and choose the Correct Tag option in the popup window displayed. When this option is selected, a window appears where you can correct the annotation.

This window contains the term, the current class and the new class, initially identical to the initial, but including a list with all the classes that can be chosen for the new class.

To change the class of the term, just select one of the classes in the given list. If you want to correct the term, simply edit the term in the given text field. If not, just click the Apply button without editing the term.

When Apply is pressed, the changes will be made.

• Notes
  • If a Lookup Table is enabled the changes are propagated to this lookup table.
  • If the All Text option is selected, all annotations for instances of this term are changed to the new class; otherwise just the selected annotation is updated

Remove Entity

If a term annotation is known to be incorrect and the term should not be annotated with any of the possible classes, the annotation can be removed within the Curator view.

To remove an annotation, just select the term and choose the option Remove Tag from the pop-up window.

• Notes
  • If a Lookup Table is enabled the changes are propagated to this lookup table.
  • If the All Text option is selected, all identical annotations are removed from the text.