A Comparative Study of Recent Ontology Visualization Tools with a Case of Diabetes Data

International Journal of Research in Computer Science
eISSN 2249-8265 Volume 2 Issue 3 (2012) pp. 31-36
© White Globe Publications
www.ijorcs.org

A COMPARATIVE STUDY OF RECENT ONTOLOGY
VISUALIZATION TOOLS WITH A CASE OF DIABETES
DATA
V. Swaminathan1, R. Sivakumar2
1
Department of Computer Science, A.V.V.M. Sri Pushpam College, Bharathidasan University,
Trichirappalli, India
Email: vswaminathanthanjavur@yahoo.com
2
Department of Computer Science, A.V.V.M. Sri Pushpam College, Bharathidasan University,
Trichirappalli, India
Email: rskumar.avvmspc@gmail.com

Abstract: Ontology is a conceptualization of a domain checking, and documentation. In the last few years, the
into machine readable format. Ontologies are number of ontology tools has greatly increased and
becoming increasingly popular modelling schemas for they have been diversified. Gomez-perez [1]
knowledge management services and applications. distinguishes the following groups:
Focus on developing tools to graphically visualise Ontology development tools group includes tools
ontologies is rising to aid their assessment and and integrated suites that can be used to build a new
analysis. Graph visualisation helps to browse and ontology from scratch. In addition to the common
comprehend the structure of ontologies. A number of edition and browsing functions, these tools usually
ontology visualizations exist that have been embedded give support to ontology documentation, ontology
in ontology management tools. The primary goal of export and import to/from different formats and
this paper is to analyze recently implemented ontology ontology languages, ontology graphical edition,
visualization tools and their contributions in the ontology library management, etc.
enrichment of users’ cognitive support. This work also Ontology evaluation tools are used to evaluate the
presents the preliminary results of an evaluation of content of ontologies and their related technologies
three visualization tools to determine the suitability of Ontology content evaluation tries to reduce problems
each method for end user applications where when one needs to integrate and use ontologies and
ontologies are used as browsing aids with a case of ontology-based technology in other information
Diabetes data. systems. Ontology merge and alignment tools are to
solve the problem of merging and aligning different
Keywords: Ontology Visualization, Semantic Web,
ontologies in the same domain. With Ontology - based
Knowledge retrieval, Reasoner. annotation tools users can insert instances of concepts
I. INTRODUCTION and of relations in ontologies and maintain
(semi)automatically ontology-based markups in web
An ontology is a formal, explicit specification of a pages. Most of these tools appeared recently, in the
shared conceptualization. Conceptualization refers to context of the semantic Web. Ontology querying tools
an abstract model of some phenomenon in the world and inference engines allow querying ontologies easily
by having identified the relevant concepts of that and performing inferences with them. Normally, they
phenomenon. Explicit means that the type of concepts are strongly related to the language used to implement
used, and the constraints on their use are explicitly ontologies.
defined. Formal refers to the fact that the ontology
should be machine-readable. Shared reflects the notion Ontology learning tools can derive ontologies
that ontology captures consensual knowledge, that is, it (semi)automatically from natural language texts, as
is not private of some individual, but accepted by a well as semi-structured sources and databases, by
group. To build ontologies is complex and time means of machine learning and natural language
consuming, and it is even more if ontology developers analysis techniques.
have to implement them directly in an ontology In recent years, number of ontology tools have been
language, without any kind of tool support. To ease designed and implemented with the support of
this task, in the mid – 1990s the first ontology building visualization. The area of cognitive assistance much
environments were created. The provided interfaces requires visualization techniques for its improvement
that helped users carry out some of the main activities in performance. Focus on developing tools to
of the ontology development process, such as graphically visualise ontologies is rising to aid their
conceptualization, implementation, consistency assessment and analysis. Graph visualisation helps to

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32 V. Swaminathan, R. Sivakumar

browse and comprehend the structure of ontologies. A evaluate the degree of cognitive support offered in
number of ontology visualizations [2] [3] exist that selected three different ontology visualization tools
have been embedded in ontology management tools with the help of end user groups.
(e.g. http://protege.stanford.edu/ and
The remaining part of this paper is organized as
http://kaon.semanticweb.org/) and are used as
follows: Section 2 gives the introduction to Protégé.
information retrieval aids in applications that use
Next Section 3 gives a survey on features
ontologies [4]. Evaluations of ontology visualization
developments in recent ontology visualization tools.
effectiveness, however, are up to this point scarce: [5]
Followed which, section 4 comes out with evaluation
presents some user experiments focused on tree
of selected tools to determine their effectiveness in
visualization systems, whereas [6] reports on
cognitive support. Section 5 concluded with future
preliminary results from a user study involving four
work.
visualization methods. They are indented list, node-
link and tree, zoomable, and focus+context. A number II. PROTEGE -2000
of visualisation techniques have been described over
the years, such as spanning tree layouts, tree-maps [7] Protege -2000 [20] is the latest version of the
fisheye views [8] , hyperbolic [9] and 3D hyperbolic protégé line of tools, created by the Stanford Medical
layouts [10], aiming to help comprehend and analyse Informatics (SIM) group at Stanford University. The
complex information structures. Preference of first protégé tool was created in 1987[21]; its main aim
visualisation models vary according to the user’s needs was to simplify the knowledge acquisition process for
and query context [11]. It is also dependant of the type expert systems. To achieve this objective, it used the
and extent of the visualised network. Using a knowledge acquired in previous stages of the process
combination of integrated visualisations of various to generate customized forms for acquiring more
types has shown to be sometimes beneficial [12][13]. knowledge. Since then, Protégé has gone through
Complex networks of multi-dimensional hierarchies several releases and has focused on different aspects of
and arbitrary relations are becoming common knowledge acquisition (knowledge bases, problem
characteristics of current ontologies. Visualising large solving methods, ontologies, etc.), the result of which
networks has always been challenging. [14][15] is protégé-2000.The history of the protégé line of tools
Surveyed a wide range of visualisation techniques and was described by Gennari and colleagues [22]. It has
concluded that all existing algorithms have a size limit around 7000 registered users. Protégé-2000 is
after which they cannot cope [16] and [17] stressed the oriented to the task of ontology and knowledge-base
importance of reducing the visualised graphs into development. It is freely available for downloading
smaller sized sub graphs that users can browse to under the Mozilla open-source license. The current
visualise other parts of the network. Ontologies are version is 1.8(April 2003). Protégé-2000 is a Java-
semantically rich by definition. Ontology visualization based standalone application to be installed and run in
should therefore turn some of these semantics more a local computer .The core of this application is the
explicit [14] Spring-layout algorithms [18] are ontology editor, described further. Protégé-2000 has
example techniques that display semantically similar an extensible architecture for creating and integrating
nodes closer to each other. Such layouts could help easily new extensions (aka plug-ins). These extensions
users to quickly recognise dense areas and interrelated usually perform functions not provided by the protégé-
objects in their ontologies and KBs. In this paper we 2000 standard distribution (other types of
conduct a survey on identifying developments of visualization, new import and export formats, etc.),
cognitive support in recently implemented ontology implement Applications that use protégé-2000
visualization tools and present a summary of various ontologies, or allow configuring the ontology editor.
features and capabilities of those tools. The purpose of Most of the plug-ins are available in the protégé Plug-
this work is to assist the researchers of ontologies to in Library, where contributions from many different
understand more about this domain and to extend their research groups can be found.
research activities in new directions. The three groups of plug-ins that can be
Information visualization [19] represents developed for protégé-2000 with actual examples of
information in a manner which aids in communication such types of plug-ins are described below:
and facilitates understanding and exploration. The The first one, Tab Plug-ins are the most common
view of tools requires the user to first understand what types in Protégé-2000, and provide functions that are
the view is attempting to show. Most innovative not covered by the standard distribution of the
visualizations suffer from lack of industry acceptance. ontology editor. To perform their task, tab plug-ins
This lack of adoption restricts meaningful evaluation extends the ontology editor with an additional tab so
of the ideas in the tool. With this concept of simplicity that users can access its functions from it. The
in mind, we need to make conscious and deliberate following functions are covered by some of the plug-
efforts to focus in identifying a tool which would focus ins available: ontology graphical visualization
on the key goals of communication and understanding, (Jambalaya tab and Onto Viz tab), ontology merge and
leveraging the techniques that best facilitate those versioning (PROMT tab), management of large on-line
goals. Hence the next purpose of this paper is to knowledge sources (UMLS and WordNet tab), OKBC

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A Comparative Study of Recent Ontology Visualization Tools with a Case of Diabetes Data 33

ontology access (OKBC tab), constraint building and node-type, arc type and search (contains, start with,
execution (PAL tab), and inference engines using end with, exact match, reg exp).
Jess[23],Prolog, FLogic, FaCT, and Algemon (Jess,
Prolog, FLORA, OIL and Algernon tabs respectively). C. 3.3 DL Query (2008)
It offers the facility of quick test definition of
The next one, Slot widgets are used to display and classes to see that they subsume the appropriate
edit slot values without the default display and edit subclasses or to test for class membership of arbitrary
facilities. There are also slot widgets for displaying descriptions without having to create named class.
images, video and audio, and for managing dates, for This tool belongs to the type Tab Widget. It is
measurement units, for swapping values between slots, designed for the application of Protégé –OWL. This
etc. tool adds effectiveness to the user’s cognitive support
Finally, Backends enables users to export and by introducing the following features: Query box,
import ontologies in different formats: RDF Schema, execute option, object properties, class hierarchy
XML, XML Schema, etc. There is a backend for window, data properties, checkboxes for super class,
storing and retrieving ontologies from databases so ancestor class, equivalent class, subclass, descendent
that not only ontologies can be stored as CLIPS files class and individuals and Query result frame.
(the default storage format used by Protégé-2000) but
they can also be stored in any database JDBC IV. STUDY OF PERFORMANCE
compatible. Recently a backend to expert and import An experiment was conducted in order to evaluate
ontologies in XML has been made available users’ satisfaction on extended features implemented
by three different ontology visualization tools. As a
III. FEATURES OF RECENT ONTOLOGY part of our real time project, we created ontologies for
VISUALIZATION TOOLS DIABETES patients’ information. The experiment
This section surveys the recently implemented described in this work was designed in order to
ontology visualization tools with a scope of extended provide useful insight concerning three research areas,
features. which are:
A. OWL2Query (2011) • The evaluation of three ontology visualization
tools- DL Query, OntoGraf and OWL2Query.
This is a conjunction query cum meta-query engine
and visualization plug-in. It facilitates the creation of • The strategies and techniques employed by the
queries using SPARQL or intuitive graph based syntax users while researching DIABETE
and valuates them using any OWL API complaint information.
reasoner. This tool belongs to the category Tab Widget • The evaluation of the DIABETES ontology
and application. This tool incorporates several new created by our research project.
features such as toolbar, prefix editor, variable editor, This paper limits the discussion to the results
layout editor, query graph, SPARQL query view, concerning the advantages and disadvantages of the
SPARQL-DL preview, result panel, edge editor, three ontology visualization tools. The focus of this
property editor and Abox, Tbox & Rbox node editors. experiment was not overall ontology management and
These help the development of effectiveness of user’s editing, but rather information retrieval and assessing
cognitive support. the stability of each method for end user applications
B. Onto Graf (2010) where ontologies are used as browsing assisters. This
section gives and overview of the performed
This tool is designed for Protégé-OWL application.
evaluation, containing brief descriptions of the
It offers support for interactively navigating the
evaluation user group, the ontology used, the query
relationships of created OWL ontologies. It supports
various layouts for automatically organizing the types used for information retrieval through the
structure of designed ontology. It is compatible with ontology, the description of the evaluation sequence
Protégé-OWL 4.1 and 4.2. It is available in various and the results.
versions like1.0.1, 0.0.5, 0.0.4, 0.0.3, 0.0.2 and 0.0.1. A. Users for Evaluation
The 1.0.1 version fixed a weird generics problem with
Java6. On the other hand the 0.0.5 version added In order to examine the effectiveness of the
support to export the current visible graph into a DOT evaluated ontology visualization, a user group with
language format file. The addition of new view for both computer skills and basic domain knowledge was
visualization OWL imports and adds support for chosen. The choice of ontology was such that all the
pinning the tool tip display to show multiple tool tips users could have at least some familiarity with
at once and this is offered by version 0.0.4. By the computers and domain. This fact ensured that there
mean-time 0.0.3 version added new tool tips exporting would not be significant differences in the
graphs as images and saving/opening graphs. This tool performance of the users due to complete lack of
incorporates additional features such as focus on knowledge of the domain. Then the ontology created
home, grid alphabet, radial, spring, tree-vertical & for the “DIABETES” domain was chosen. Most of the
horizontal directed, zoom-in, zoom-out, no-zoom, users that participated to the experiment were the

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research scholars of Computer Science and characteristics etc. The identified query types are
Information Science departments of Sri Pushpam presented in the following text, along with brief
College of Bharathidasan University, India. All these description examples.
users have some knowledge both in computers and
1. The user is given the value of a slot of an instance,
DIABETES domain as they are instructed to be
familiar for testing. But they vary in degree of skills and is asked to find the value of another slot of the
both in computer and domain knowledge respectively. same instance. For example, “What is the year of
The user group was divided into two commensurate registration of the patientid 101?”
groups of eight users one that got a short introduction In this case the user has to locate a specific instance
in how to use these testing tools, and one without any and then extract a slot value to find the answer to the
prior knowledge about ontology editing. query.
B. Ontology Description 2. The user is given the value of a slot of an instance
The ontology used in this experiment is an effort to I1, and is asked to retrieve a slot value of some
describe the domain of the DIABETES - instance I2, linked to I1 through a role relationship.
THANJAVUR. It presents the current DIABETES For example, “What is the year of identification of the
patients information under the treatment and also Type 1 that a particular patient affected with?”
contains relevant information about the symptoms and In this case the user should first locate I1, follow the
causes of DIABETES. It contains 15 classes. It is role relationship to I2 and then extract a slot value to
populated with 257 instances. The maximum depth of find the answer to the query.
the “is-a” taxonomy tree is 13 classes. Multiple
inheritances have been employed for about 2 classes 3. Query related to the class hierarchy, the taxonomy.
and no other classes are having more than one parent. In this case, a class is described to the user and he/she
is asked to retrieve its direct subclasses. For example,
C. Experimental set-up
“What are the symptoms of the “Type 1”?
Before starting the evaluation process we had to In this example, the result is a set of class names,
perform some preliminary tests in order to decide upon which should be organized hierarchically.
the visualization method set-up to be used in the
experiment. 4. Querying for the number of instances of a specific
class. For example, “What is the number of the drug
Bearing in mind that we were investigating the
most suitable visualization not for ontology developers manufacturer?”
but for users that will use the ontology as an In this case the result is a number, so the user has to
information retrieval aid, we had to keep the locate the specific instances and count them or view
visualization method controls as simple as possible. their number if this feature is provided by the
Furthermore, for the size of the experiment ontology, interface.
some visualization set-ups were really cluttered and 5. Retrieve the number of instances with a specific
not at all useful for information retrieval. In the case of common slot value. For example, “What is the number
DLQuery, Query box, execute option; object of patients prescribed with a specific drug?”
properties, class hierarchy window, data properties,
checkboxes for super class, ancestor class, equivalent In this case, as in query 4 of the previous section,
class, subclass, descendent class and individuals and the result is a number, so the user has to locate the
Query result frame were introduced to the users. In the specific instances and count them (or view their
case of OntoGraf, focus on home, grid alphabet, radial, number if this feature is provided by the interface).
spring, tree-vertical & horizontal directed, zoom-in, However, this case is somewhat more complicated as
zoom-out, no-zoom, node-type, arc type and search not all the instances of an entity are requested, but a
(contains, start with, end with, exact match, reg exp) sub-set of them with a common slot value. The user
options were introduced to the users. Finally, for the groups were involved in retrieving the answers for
case of OWL2Query, we introduced the following those queries using DL Query, OWL2Query and
features to the users: toolbar, prefix editor, variable OntoGraf.
editor, layout editor, query graph, SPARQL query
E. Performance Evaluation
view, SPARQL-DL preview, result panel, edge editor,
property editor and Abox, Tbox & Rbox node editors. For each task (query), we measured the NASA
Task Load Index (TLX) [24] and the time that was
D. DIABETES ontology information retrieval tasks needed to perform the task. Figure 1 show the results
This experiment constructed five different queries of the comparison of OWL2Query, DLQuery and
to retrieve information from DIABETES ontology. OntoGraf ontology visualization tools based on the
The queries are then grouped into different types visualization scores as perceived by the users. As we
according to ontology related criteria, such as the expected, we can see that the group that was given a
number of different classes they entail, if they are short introduction into the tools, performed better on
relevant to the ontology hierarchy or not, if they ask average. It scored lower TLX and shorter time.
for the number of classes of instances with a common

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A Comparative Study of Recent Ontology Visualization Tools with a Case of Diabetes Data 35

For task1, there was almost no difference observed also included in its analysis information about the
between the two groups with respect to Onto Graf. The import/export format, graph view, consistency check,
figure 1 clearly shows Onto Graf let to a lower TLX on version, dependencies, type, multi-user type, web
average in all five tasks compared to other two tools support, library support and etc., The result of this
such as OWL2Query and DLQuery, that is, users were survey and analysis provides comprehensive
less frustrated and mentally stressed. That is very understanding of new features that enhance cognitive
likely also an outcome of the reduced time users had to support. Finally, we presented some preliminary
spend for each task. The figure shows that users could results from a comparative evaluation of selected three
solve each task faster using Onto Graf. On average visualization tools. The results are being further
users spent approximately 58.9 % less time with Onto analyzed in order to extract interesting patterns.
Graf and had a 24.9% lower TLX than when using Furthermore, the results of this evaluation are being
OWL2Query and 32.8 % less time with Onto Graf and analyzed with respect to the other two aspects of the
had a 15.9% lower TLX than when using DLQuery. experiment, i.e. the evaluation of the ontology itself
The comparison only shows that Onto Graf is better and a test of the methods users employ for dealing
suited for the use case of DIABETES ontology we with various information retrieval types. This work can
described. DLQuery and OWL2Query are however be extended with other tools/ frameworks for the
much more feature enriched tools which make it complete ontology management operations
difficult to use than Onto Graf for our experiment. We
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