Chapter 5
Visual CREOLE [#]
...neurobiologists still go on openly studying reflexes and looking under the hood, not huddling passively in the trenches. Many of them still keep wondering: how does the inner life arise? Ever puzzled, they oscillate between two major fictions: (1) The brain can be understood; (2) We will never come close. Meanwhile they keep pursuing brain mechanisms, partly from habit, partly out of faith. Their premise: The brain is the organ of the mind. Clearly, this three-pound lump of tissue is the source of our ”insight information” about our very being. Somewhere in it there might be a few hidden guidelines for better ways to lead our lives.
Zen and the Brain, James H. Austin, 1998 (p. 6).
This chapter details the other visual resources that can be used in GATE. While these tools were not included as part of earlier releases of GATE, as of GATE version 3.0, they are included as part of the standard release, and are now open source. GAZE, Ontogazetteer and the Protégé VR for GATE were all developed by Ontotext, who should be contacted for further information about these components.
5.1 Gazetteer Visual Resource - GAZE [#]
Gaze is a tool for editing the gazetteer lists, definitions and mapping to ontology. It is suitable for use both for Plain/Linear Gazetteers (Default and Hash Gazetteers) and Ontology-enabled Gazetteers (OntoGazetteer). The Gazetteer PR associated with the viewer is reinitialised every time a save operation is performed. Note that GAZE does not scale up to very large lists (we suggest not using it to view over 40,000 entries and not to copy inside more than 10, 000 entries).
5.1.1 Running Modes
The running mode depends on the type of gazetteer loaded in the VR. The mode in which Linear/Plain Gazetteers are loaded is called Linear/Plain Mode. In this mode, the Linear Definition is displayed in the left pane, and the Gazetteer List is displayed in the right pane. The Extended/Ontology/Mapping mode is on when the displayed gazetteer is ontology-aware, which means that there exists a mapping between classes in the ontology and lists of phrases. Two more panes are displayed when in this mode. On the top in the left-most pane there is a tree view of the ontology hierarchy, and at the bottom the mapping definition is displayed.
5.1.2 Loading a Gazetteer
To load a gazetteer into the viewer it is necessary to associate the Gaze VR with the gazetteers. Afterwards whenever a gazetteer PR is loaded, Gaze will appear on double-click over the gazetteer in the Processing Resources branch of the Resources Tree.
5.1.3 Linear Definition Pane
This pane displays the nodes of the linear definition, and allows manipulation of the whole definition as a file, as well as the single nodes. Whenever a gazetteer list is modified, its node in the linear definition is coloured in red.
5.1.4 Linear Definition Toolbar
All the functionality explained in this section (New, Load, Save, Save As) is accessible also via File — Linear Definition in the menu bar of Gaze.
New – Pressing New invokes a file dialog where the location of the new definition is specified.
Load – Pressing Load invokes a file dialog, and after locating the new definition it is loaded by pressing Open.
Save – Pressing Save saves the definition to the location from which it has been read.
Save As – Pressing Save As allows another location to be chosen, and the definition saved there.
5.1.5 Operations on Linear Definition Nodes
Double-click node – Double-clicking on a definition node forces the displaying of the gazetteer list of the node in the right-most pane of the viewer.
Insert – On right-click over a node and choosing Insert, a dialog is displayed, requesting List, Major Type, Minor Type and Languages. The mandatory fields are List and Major Type. After pressing OK, a new linear node is added to the definition.
Remove – On right-click over a node and choosing Remove, the selected linear node is removed from the definition.
Edit – On right-click over a node and choosing Edit a dialog is displayed allowing changes of the fields List, Major Type, Minor Type and Languages.
5.1.6 Gazetteer List Pane
The gazetteer list pane has a toolbar with similar to the linear definition’s buttons (New, Load, Save, Save As). They work as predicted by their names and as explained in the Linear Definition Pane section, and are also accessible from File / Gazetteer List in the menu bar of Gaze. The only addition is Save All which saves all modified gazetteer lists. The editing of the gazetteer list is as simple as editing a text file. One could use Ctrl+A to select the whole list, Ctrl+C to copy the selected, Ctrl+V to paste it, Del to delete the selected text or a single character, etc.
5.1.7 Mapping Definition Pane
The mapping definition is displayed one mapping node per row. It consists of a gazetteer list, ontology URL, and class id. The content of the gazetteer list in the node is accessible through double-clicking. It is displayed in the Gazetteer List Pane. The toolbar allows the creation of a new definition (New), the loading of an existing one (Load), saving to the same or new location (Save/Save As). The functionality of the toolbar buttons is also available via File.
5.2 Ontogazetteer [#]
The Ontogazetteer, or Hierarchical Gazetteer, is an interface which makes ontologies “visible” in GATE, supporting basic methods for hierarchy management and traversal. In GATE, an ontology is represented at the same level as a document, and has nodes called classes (for consistency with RDFs ad DAML+OIL, though they are really just types). The OntoGazetteer assigns classes rather than major or minor types, and is aware of mappings between lists and class IDs. There are two Visual Resources, one for editing the standard gazetteer lists (including the definition files and the mappings to the ontology), and one for editing the ontology itself.
5.2.1 Gazetteer Lists Editor and Mapper [#]
This is a VR for editing the gazetteer lists, and mapping them to classes in an ontology. It provides load/store/edit for the lists, load/store/edit for the mapping information, loading of ontologies, load/store/edit for the linear definition file, and mapping of the lists file to the major type, minor type and language.
Left pane: A single ontology is visualized in the left pane of the VR. The mapping between a list and a class is displayed by showing the list as a subclass with a different icon. The mapping is specified by drag and drop from the linear definition pane (in the middle) and/or by right click menu.
Middle pane: The middle pane displays the nodes/lines in the linear definition file. By double clicking on a node the corresponding list is opened. Editing of the line/node is done by right clicking and choosing edit: a dialogue appears (lower part of the scheme) allowing the modification of the members of the node.
Right pane: In the right pane a single gazetteer list is displayed. It can be edited and parts of it can be cut/copied/pasted.
5.2.2 Ontogazetteer Editor [#]
This is a VR for editing the class hierarchy of an ontology. it provides storing to and loading from RDF/RDFS, and provides load/edit/store of the class hierarchy of an ontology.
Left pane: The various ontologies loaded are listed here. On double click or right click and edit from the menu the ontology is visualized in the Right pane.
Right pane: Besides the visualization of the class hierarchy of the ontology the following operations are allowed:
- expanding/collapsing parts of the ontology
- adding a class in the hierarchy: by right clicking on the intended parent of the new class and choosing add sub class.
- removing a class: via right clicking on the class and choosing remove.
As a result of this VR, the ontology definition file is affected/altered.
5.3 The Document Editor [#]
The document editor is contained in the central tabbed pane as seen on figure 5.1. It consist of a top panel with buttons and icons that control the display of different views and the search box.
The central part is the text view, then at the bottom there is the annotations list view and at the left the annotation sets view which can be replaced with the co-reference editor.
These views are describe in the next subsections so we will now focus only on the annotation editor popup window that you can see in the middle of the document editor.
The annotation editor consist of different action icons at the top then a drop down box for the annotation type, a table of features names and values and finally a disclosure panel for the search and annotate function.
To grow/shrink the span of the annotation at its start use the two arrow icons on the left or Right and Left keys. Use the two arrow icons next on the right to change the annotation end or Alt+Right and Alt+Left keys. Add Shift and Control+Shift keys to make the span increment bigger. The red X icon is for removing the annotation and the pin icon is to pin the window so it doesn’t move when you select another annotation.
All the views are updated each time an annotation change. There is more than one way to create or edit annotations so try to find the best for your task. For example, if you want to delete all the annotations of one type that are at the beginning of a document you can use the annotations list view, then sort it by start offset, select the rows to delete and right-click for the context menu to delete the selection. It will be much faster than selecting each annotation in the document editor and delete it.
For more information on how to create and edit annotations or search and annotate the document see section 3.19.
See also section 12.2.2 for the compound document editor.
5.3.1 The Annotation Sets View [#]
The annotation sets view is displayed on the left part of the document editor. It’s a tree-like view with a root for each annotation set. The first annotation set being the default one without name.
To display all the annotation of one type tick its checkbox or use Space key. To delete an annotation type use Delete key. To change the color use Enter key. There is a context menu for all these actions that you can display by right-clicking on one annotation type, a selection or an annotation set.
To create a new annotation set use the text field at the bottom and the ’New’ button.
5.3.2 The Annotations List View [#]
The annotations list view is displayed at the bottom of the document editor. It’s a table of all the highlighted annotations in the document. You can sort the table by clicking on the headers and hide some column by right-clicking on the headers.
A context menu is available on the selected rows and allow to delete annotations or display one or more annotation editor.
5.3.3 The Co-reference Editor [#]
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The co-reference editor allows co-reference chains (see section 8.8) to be displayed and edited in the GATE GUI. To display the co-reference editor, first open a document in GATE, and then click on the Co-reference Editor button in the document viewer.
The combo box at the top of the co-reference editor allows you to choose which annotation set to display co-references for. If an annotation set contains no co-reference data, then the tree below the combo box will just show ’Coreference Data’ and the name of the annotation set. However, when co-reference data does exist, a list of all the co-reference chains that are based on annotations in the currently selected set is displayed. The name of each co-reference chain in this list is the same as the text of whichever element in the chain is the longest. It is possible to highlight all the member annotations of any chain by selecting it in the list.
When a co-reference chain is selected, if the mouse is placed over one of its member annotations, then a pop-up box appears, giving the user the option of deleting the item from the chain. If the only item in a chain is deleted, then the chain itself will cease to exist, and it will be removed from the list of chains. If the name of the chain was derived from the item that was deleted, then the chain will be given a new name based on the next longest item in the chain.
A combo box near the top of the co-reference editor allows the user to select an annotation type from the current set. When the Show button is selected all the annotations of the selected type will be highlighted. Now when the mouse pointer is placed over one of those annotations, a pop-up box will appear giving the user the option of adding the annotation to a co-reference chain. The annotation can be added to an existing chain by typing the name of the chain (as shown in the list on the right) in the pop-up box. Alternatively, if the user presses the down cursor key, a list of all the existing annotations appears, together with the option [New Chain]. Selecting the [New Chain] option will cause a new chain to be created containing the selected annotation as its only element.
Each annotation can only be added to a single chain, but annotations of different types can be added to the same chain, and the same text can appear in more than one chain if it is referenced by two or more annotations.
