1
Jambalaya: Interactive visualization to enhance
ontology authoring and knowledge acquisition in Protégé
Margaret-Anne Storey1,4 Mark Musen2 John Silva3
Casey Best1 Neil Ernst1 Ray Fergerson2 Natasha Noy2

Abstract
This paper describes the integration of an interactive visualization user interface with a knowledge management
tool called Protégé. Protégé is a general-purpose tool that allows domain experts to build knowledge-based systems by
creating and modifying reusable ontologies and problem-solving methods, and by instantiating ontologies to construct
knowledge bases. The SHriMP (Simple Hierarchical Multi-Perspective) visualization technique was designed to
enhance how people browse, explore and interact with complex information spaces. Although SHriMP is information
independent, its primary use to date has been for visualizing and documenting software programs. The paper describes
how we have applied software visualization techniques to more general knowledge domains. It is hoped that the
integrated environment (called Jambalaya) will result in an easier to use and more powerful environment to support
ontology evolution and knowledge acquisition. An example scenario of how Jambalaya can be applied to knowledge
acquisition is provided.
1 Introduction
This paper describes how we have integrated an interactive visualization user interface with a knowledge
management tool called Protégé. The Protégé environment has been developed at Stanford University over the past 16
years [1, 2, 3]. It supports the modeling of ontologies and use of ontologies to guide acquisition of content knowledge
from subject-matter experts. Moreover it allows developers to easily “plug-in” components to add new functionalities
to the Protégé tool. Protégé is being actively used by hundreds of users world-wide in many knowledge domains.
An ontology defines a common
vocabulary and structure of an information
space for researchers and domain experts to
exchange and share knowledge. A domain
expert defines classes to represent concepts
in a domain of discourse, with slots to
represent properties and relationships
between the concepts. An ontology together
with a set of instances constitutes a
knowledge base. A class can have
subclasses to represent more specific
concepts.
Figure 1 shows the ontology editing
environment in Protégé. The class hierarchy
is shown on the left side of the pane, with the
form for editing properties of the class
depicted on the right hand side. The
ontology example used throughout this paper
is a food and wine example as described in
[4]. In Fig. 1, the class highlighted on the
left pane is the “Meal Course” class. The
form on the right shows the properties (slots) depicting relationships between this class and instances of this class type

1 Department of Computer Science, University of Victoria.
2. Stanford Medical Informatics, Stanford University.
3. National Cancer Institute.
4. Department of Aeronautics and Astronautics, MIT.
Email contacts: mstorey@csr.uvic.ca; musen@smi.stanford.edu
Figure 1: The ontology editing tab in Protege

2
Figure 2: This figure shows the instance tab in Protégé.
have with other instances and classes in the knowledge base.
Figure 2 shows the instances tab in
Protégé. In this tab, the class hierarchy
along with the instances of a selected
class are shown in the two leftmost
columns. The column on the right side
contains the form for that instance
revealing the values for the slots of the
instance’s class. Here we see an
instance of the “Meal Course” class
called “Grilled Chicken”. The “Food”
and “Drink” slots (defined by the
instantiating class as shown in Fig. 1)
have values corresponding to “Grilled
Chicken” and “Beaujolais”
respectively. Instance forms are used
to enable knowledge acquisition.
Forms can be customized by the
developer when classes are defined.
Understanding and maintaining the
structure of large knowledge bases has
been a problem since the days of
MYCIN [5]. Many knowledge bases
contain very complex structures that need to be viewed at various levels of abstraction and in different contexts to be
truly understood. Indeed, the underlying model of any knowledge base is just one interpretation of the knowledge to be
modeled and may not reflect another individual’s or organization’s perception of the information space. Consequently,
knowledge acquisition can be a cognitively challenging task as the user has to have a clear understanding of the
ontology as well as manage detailed information.
Several Protégé users (most recently at [6]) expressed the need for tools that provide visualizations of the coarser
grained structures in the knowledge base as well as provide mechanisms to more easily and more efficiently navigate
the information. Some knowledge base tools (including Protégé) do provide some primitive or restrictive visualization
capabilities. However, they tend to be either domain or task specific views that are either difficult to customize or do
not scale to large, complex knowledge bases. An early visualization tool called SemNET [7], although promising, was
not adopted by the general community. SemNET, a proprietary tool, required (at that time) fairly advanced hardware to
produce interactive views.
Some of the problems reported to us by Protégé users include disorientation as they navigate through large,
complex ontologies. Unwieldy screen clutter often occurs due to many separate window frames being opened. These
kinds of difficulties are also shared by users of other tools that deal with large amounts of information. In this paper we
describe and discuss the integration of a visualization technique, called SHriMP Views, using Protégé’s plug-in facility.
SHriMP’s primary benefits include generic visualization techniques and navigation facilities to make better use of
people’s cognitive abilities when using a screen of fixed size.
The rest of the paper is organized as follows. Section 2 provides some brief background on the SHriMP
visualization technique. Section 3 describes how we have integrated SHriMP with Protégé, we refer to this integration
as Jambalaya. A scenario is used to help describe how Jambalaya can be used in ontology authoring and knowledge
acquisition in Section 4. Section 5 discusses the visualization capabilities provided by this integration and describes our
plans for future work.
2 SHriMP Views
The SHriMP (Simple Hierarchical Multi-Perspective) visualization technique was designed to enhance how people
browse, explore, model and interact with complex information spaces [8]. SHriMP uses a nested graph view to present
information that is hierarchically structured. It introduces the concept of nested interchangeable views to allow a user to
explore multiple perspectives of information at different levels of abstraction. SHriMP combines a hypertext following
metaphor with animated panning and zooming motions over the nested graph to provide continuous orientation and
contextual cues for the user. These features result in an environment where the user can interact directly with the
information space enhancing their understanding of the information structures, thus promoting further exploration.