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. 2007 Nov;20 Suppl 1(Suppl 1):34-46.
doi: 10.1007/s10278-007-9065-0. Epub 2007 Aug 9.

Protégé: a tool for managing and using terminology in radiology applications

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Protégé: a tool for managing and using terminology in radiology applications

Daniel L Rubin et al. J Digit Imaging. 2007 Nov.

Abstract

The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The development and maintenance of these terminologies are challenging, however, because there are few specialized tools to help developers to browse, visualize, and edit large taxonomies. Protégé ( http://protege.stanford.edu ) is an open-source tool that allows developers to create and to manage terminologies and ontologies. It is more than a terminology-editing tool, as it also provides a platform for developers to use the terminologies in end-user applications. There are more than 70,000 registered users of Protégé who are using the system to manage terminologies and ontologies in many different domains. The RadLex project has recently adopted Protégé for managing its radiology terminology. Protégé provides several features particularly useful to managing radiology terminologies: an intuitive graphical user interface for navigating large taxonomies, visualization components for viewing complex term relationships, and a programming interface so developers can create terminology-driven radiology applications. In addition, Protégé has an extensible plug-in architecture, and its large user community has contributed a rich library of components and extensions that provide much additional useful functionalities. In this report, we describe Protégé's features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology.

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Figures

Fig 1
Fig 1
A Protégé “frame.” This screen capture shows a frame in Protégé representing the class in RadLex (a RadLex term). The class contains several slots (attributes the contained values), such as a preferred name of “supraaortic valve area,” an internal RadLex identifier name (“RID482”), a version number, definition, and other information such as the arterial segment of which it is a part, synonyms, and other information about the term.
Fig 2
Fig 2
A Protégé “slot.” This screen capture shows a frame in Protégé representing the slot called “Name,” which is used to convey the unique identifier name for a RadLex term. This name slot contains facetscomponents that constrain its values such as cardinality, value type, minimum, and maximum values. In this case, the facet values are saying that Name is a single-valued string, and it must have a value for every term in RadLex. This slot is associated with all classes in RadLex; for example, for the supraaortic valve area class (Fig. 1), this slot has a value of “RID482.” Another slot called Preferred Name is used to store the actual name of the class, “supraaortic valve area” (Fig. 1).
Fig 3
Fig 3
Protégé architecture. Protégé is built using a tiered architecture. The Protégé knowledge model is an object-oriented model (“OO Model”) of ontologies stored in a persistence layer (DB storage) and accessed via the Protégé API. The API is used both by the protégé GUI application (View layer) with which users access the ontologies, as well as by application programs (Application layer). New functionality is added to Protégé by creating plug-ins, which access ontologies through the Protégé API and with which the user can interact by plugging into the Protégé GUI.
Fig 4
Fig 4
RadLex shown in the main Protégé user interface, which provides the ability to build, populate, and view ontologies and terminologies. This screen capture shows the Classes tab, in which the user creates, edits, and browses the terms in RadLex. The taxonomy of Radlex is shown as an expandable tree on the left. The right panel displays the details of a RadLex term selected from the tree on the left. For each class selected, Protégé displays the attributes of that class (right) which users can edit. For example, the left coronary sinus has been selected (left) and it is a branch of the supraaortic valve area. Other tabs in the Protégé GUI include: the Slots tab, for creating and editing slots; the Forms tab, for customizing layout of knowledge-entry forms (such as the one shown on the right); the Instances tab for creating instances of classes and entering particular slot values for those instances; and any other special-purpose “plug-in” tab that the user may want to use.
Fig 5
Fig 5
Displaying changes in PromptDiff. The output from PROMPT is shown in after comparing RadLex with a version of the terminology that was edited to move a class, change its name, and add a slot value. Left panel: Changes to the class hierarchy are shown. Different styles represent different types of changes: added class is underlined and in blue; moved classes are flagged out in their old positions and appear in bold in their new ones. Right panel: Individual changes to the slot values for a selected class are shown (in this case, for the supraaortic area class).
Fig 6
Fig 6
Visualizing RadLex using the OntoViz plug-in for Protégé. This visualization plug-in for Protégé displays an ontology as a graph (right panel). Ontology classes are shown as boxes, and the relationships among them are shown as arcs. The label on the arc is the name of the relationship. The user can select the classes to be displayed in the graph (lower left panel) as well as the types of information to display, such as subclasses, superclasses, and relationships (upper left panel). This visualization paradigm is particularly helpful when an ontology contains more than one type relationship, since the tree view (left) only shows the ontology classes according to one relationship (is-a).
Fig 7
Fig 7
Visualizing RadLex using the TGVizTab plug-in for Protégé. The TGViz plug-in to Protégé displays an ontology as a TouchGraph (right panel), enabling the user to navigate the ontology as a nested, zoomable graph. The graph is initially created by selecting a root class from the tree view (upper left panel); the root class is shown in the center of the graph (right panel). Classes are shown as the names of the class, and the relationships between classes are shown as arcs, with the type of relationship appearing when the mouse passes over the arcs (upper left part of graph in right panel). Users navigate the ontology by double-clicking on a class name in the graph, which zooms into that class, producing a new TouchGraph rooted at that class.
Fig 8
Fig 8
Collaborative Protégé. Protégé supports collaborative ontology editing by permitting users to annotate ontology components as well as ontology changes. It also supports searching and filtering of user annotations based on different criteria. In this screenshot, a user has identified a duplicate term in RadLex and communicates that to the curators by creating an annotation on the term in question (“Brodmann area 6”). The term to be annotated is selected (left panel), and annotations are created (right panel) to describe the user’s feedback. The RadLex curator can search, filter, and browse annotations created by the community, and create annotations serving as to-do items for incorporating changes and suggestions in future releases of RadLex. This screenshot shows that the curator agrees with the user feedback and creates an annotation reflecting the need for the duplicate term to be removed in the next release of RadLex.
Fig 9
Fig 9
Programmatically interacting with ontologies using the Protégé Script Tab. This screen shot shows some example interactive commands to the Protege API and their results.
Fig 10
Fig 10
RadLex ontology accessed over the Internet using WebProtege. This application provides Web access to ontologies; a single ontology file can be edited by curators (Fig. 1) and immediately deployed on the Web without needing to update any software applications. The ontology is shown on the left, and details about selected terms on the right, similar to that provided by the Protégé editing tool (Fig. 4).

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