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RDF Graph Visualization Tools: a Survey

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Semantic Web technologies are increasingly being used for the development of Future Internet applications, mainly due to the impressive growth of the Internet of Things research area. This spread pushes for effective and efficient ways to visualize the content of RDF ontologies and knowledge bases. Several strategies can be adopted to visualize semantic data and one of this consists in exploiting the graph representation intrinsic in the RDF model. In this paper, we propose a survey of the main tools for the graphical visualization of triples (being them terminological or assertional statements) exploiting a graph representation.
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RDF Graph Visualization Tools: a Survey
Francesco Antoniazzi
INFN CNAF and University of Bologna
Bologna, Italy
francesco.antoniazzi@unibo.it
Fabio Viola
University of Bologna
Bologna, Italy
fabio.viola@unibo.it
Abstract—Semantic Web technologies are increasingly being
used for the development of Future Internet applications, mainly
due to the impressive growth of the Internet of Things research
area. This spread pushes for effective and efficient ways to
visualize the content of RDF ontologies and knowledge bases.
Several strategies can be adopted to visualize semantic data
and one of this consists in exploiting the graph representation
intrinsic in the RDF model. In this paper, we propose a survey
of the main tools for the graphical visualization of triples (being
them terminological or assertional statements) exploiting a graph
representation.
I. INTRODUCTION
The Semantic Web [1] movement was born to transform
the Web from a repository of human-readable information,
to a world wide network of machine-understandable data. To
achieve the scope, multiple protocols were introduced: RDF
(Resource Description Framework) [2] allows to represent all
the information as a set of triples (i.e., subject,predicate,
object) where resources are univocally identified through URIs
(Uniform Resource Identifiers). Ontologies represented ac-
cording to RDFS (RDF Schema) [3] and OWL (Web Ontology
Language) [4] bind meanings to RDF terms (with a set of
rules expressed through RDF). Finally, SPARQL Query [5]
and Update [6] languages allow to respectively retrieve data
from the Knowledge Base (KB) and update it.
Semantic Web technologies are gaining momentum, due to
the wide spread of two strongly linked research areas: context-
aware computing [7] and the Internet of Things (IoT) [8].
Context-aware computing is aimed at developing applications
able to adapt to changes in the environment and often exploits
semantics to model the context with a high expressive power.
The IoT is instead a world-wide network of interconnected and
uniquely addressable objects, based on given communication
protocols [9]. It is characterized by heterogeneity of the
involved devices and by a multitude of protocols born with
different aims [10]. For this reason, IoT applications are almost
always compared to vertical silos [11] where the interoper-
ability is a challenging task. In this scenario, Semantic Web
technologies are often considered as interoperability enablers
that allow to bridge different applications by means of a
semantic representation of the involved entities.
Then, also thanks to context-aware computing and IoT, the
number of applications exploiting Semantic Web technologies
is costantly increasing, as demonstrated by LOV (Linked Open
Vocabulary) [12], an innovative observatory of the semantic
vocabularies ecosystem. Vandenbussche et al. in [13] describe
the impressive growth of the repository: less than 100 on-
tologies in March 2011, more than 500 as of June 2015 (as
of September 2018, the number is growth up to 650). Given
the high spread of semantic applications, it is essential for
both developers and users to have efficient tools to visualize
ontologies as well as to explore semantic KBs.
Before going further, it is important to clarify two of the
key concepts that we will rely on in the rest of the paper
and that we already mentioned: ontology and knowledge
base. Among the multiple definitions of ontology available
in literature, we rely on the one provided by Noy et al. in
[14]: an ontology is a formal explicit description of concepts
in a domain of discourse (classes), properties of each concept
describing various features and attributes of the concept and
restrictions. Since an OWL/RDFS ontology is represented as
a set of RDF triples, we refer to these triples as terminological
statements (or T-Boxes). All the triples defining and specifying
class instances are instead known in literature as assertional
statements (or A-Boxes). A-Boxes and T-Boxes form the
knowledge base.
In the rest of the paper we will consider the visualization
of data from two (possibly overlapping) points of view:
visualization of ontologies and visualization of RDF triples
represented according to a given ontology. While the first
is aimed at grasping the relevant concepts of an application
domain, the second is mostly aimed at a practical inspection of
data (e.g., for debug purposes). In both cases it is important to
be able to dominate the complexity of a very high amount of
data by means of proper visualization strategies and effective
filtering mechanisms.
In this paper, we survey the available software aimed at
providing a graphical visualization of semantic knowledge
bases containing either terminological or assertional data.
We focus only on the tools adopting the graph metaphor to
represent data (other possible graphical representation methods
are briefly p resented in S ection III).
The rest of the paper is organized as follows: in Section II,
an overview of the existing surveys on the visualization of
semantic knowledge bases is proposed. Section III introduces
the background for this work and motivates the need for a
new survey in this research area. Section IV presents the
main tools for the visualization of Semantic Web datasets. For
tools still actively developed and/or widely used, this paper
also proposes examples based on information retrieved from
DBpedia. In Section V, all the features of the analyzed tools
are summarized. Eventually, in Section VI, conclusion are
drawn.
II. RELATED WORK
The graphical representation of information is a topic that
has been addressed in various ways by research, since it is a
matter of algorithms and user interface theory simultaneously,
and, as pointed out in [15], nowadays also of Big Data.
Literature is rich in surveys and explorations of visualization
methods for information represented according to Semantic
Web technologies. The Semantic Web, in particular, relies
on the graph theories for what concerns the viewing of
knowledge, which is a topic well covered by surveys like [16].
However, the actual investigation of the Semantic content,
most of the time, is centered on the usage and integration
of ontologies in applications, like in [17] and [18]. Semantic
content visualization, on top of them, is a particular research
topic that tries to overcome the difficulties that a rise at devel-
opment time when direct usage and integration is required.
In their survey [19], Katifori et al. point out the need
for studies in the visualization field at the v arious l evels of
usage of semantics: design, organization and navigation into
resources. Similarly is done by Mutton et al. in [20], where the
complexity of graph drawing is examined keeping in mind that
there is implicit information hidden in a graph topology that
cannot be easily observed from a plain textual representation.
Another work, in this sense, is [21] by Wiens et al., in which
the ontology view is split into three levels of understanding:
global, filtered and m ore s pecific bu t fu lly detailed.
The main discussion of those works, however, is the on-
tology: a complete outline of methods is given, but the full
content of the RDF knowledge base is out of the scope.
In [22], Bikakis et al. propose a description of the major
requirements and challenges that should be addressed by
modern exploration and visualization systems for Linked Data
and propose a list of the state of the art approaches. Differ-
ently from the present work, they propose a comparison of
tools offering different visualization types (i.e., bubble charts,
charts, circles, graphs, maps, pies, parallel coordinates, scatter
plots, streamgraphs, treemaps, timelines, trees) and the focus is
mainly on Big Data applications. Akrivi et al. in [23] propose
a comparison of four visualization methods (i.e., Ontoviz,
Jambalaya, TGVizTab and Class Browser) characterized by
different approaches. In [24], an interesting study is performed
with the aim to explore pros and cons of the available tools
on a real use case.
Along with tools, plain text formats for the Semantic Web
are also subject to evolution over time. Recently, for instance,
JSON-LD (standing for JSON for Linked Data) was introduced
in the Semantic environment [25] as a new format graph-
equivalent to represent part of a resource graph. The official
JSON-LD W3C website [26], among all the material, offers
also the opportunity to compare a few different visualizations
obtained from any JSON-LD formatted file.
The Linked Data (LD) concept, described in [27], is a
more recent research direction on Semantic Web applied to
web resources. LD are constantly growing in size and new
data repositories, that come also from governmental sources,
which demonstrates their increasing importance. The final goal
is to have LD both machine and human understandable, and
therefore, they are an important test bench for any RDF graph
visual exploration technique. Pe˜
na et al. in their work [28]
intent the description of the available methods to deal with
LD access and, in particular, the visualization.
III. BACKGROUND AND MOTIVATION
Accessing and understanding the content of a database is
hardly ever a negligible task for programmers. When data
is stored in a relational database, the views are obtained by
transforming into a table the output of a query written in one of
the various flavors of the SQL language. Smart-written queries
on equally smart-built databases can efficiently perform a lot of
calculations over data, as well as outline special and complex
relationships even between apparently distant entries. There-
fore the know-your-data principle, typical of Data Mining and
Big Data theory, is in fact a more general and solid base
from which to start any data-related implementation, though
implying sometimes great study effort from the developer in
the initial phase of software creation [29]. It is, as a matter
of fact, common knowledge that frequently programmers have
to spend more time in organizing and reformatting their data
more than in the actual programming logic.
As of September 2018, this Survey aims to show to the
readers the tools currently available to exploit in an effective
and possibly easy way the Semantic Web. Therefore, the focus
of the paper is the observation of their overall usability and
capabilities in the complex task of analyzing and understand-
ing the content of a knowledge base. For this reason, both the
ontological statements (T-Boxes) and the instances (A-Boxes)
have to be included in the discussion, which is a missing point
in the previous similar works, as we outlined in the Related
Works Section.
A. Representing data in the Semantic Web
The appearance of the Semantic Web in the panorama of
information technology gave ways more than a simple new
tool to explore the Web, but a new interpretation of the
resources available on the Internet. Through the SPARQL lan-
guage and the Resource Description Framework, the Internet
network is considered as a whole a special database whose
resources are interconnected in a labeled directed graph. The
main idea of the Semantic Web, therefore, is to exploit the
concepts of Uniform Resource Identifier, e xplained in [ 1], to
bind resources through triple-based statements (i.e., the already
mentioned subject-predicate-object triple). Any connection is
in that fashion not a simple reference as hypertext linking
is, but contains in addition the information given by the
inner content of the resources. Then, according to W3C
recommendations [30], the Semantic Web in the end takes the
form of a graph, where both the contents and the statements
contribute to the overall meaning. Table I shows what kind of
TABLE I
SEMANTIC TRIPLE COMPOSITION WITH AN EXAMPLE
Subject Predicate Object Example
URI URI URI ns:Francesco foaf:knows ns:Fabio
literal ns:Francesco foaf:firstName "Francesco"
blank node ns:Francesco foaf:knows _:X
blank node URI URI _:X foaf:knows ns:Francesco
literal _:X foaf:firstName "Francesco"
blank node _:X foaf:knows _:Y
TABLE II
LISTING 2 SPARQL OUTPUT TABLE
?p ?count
<http://purl.org/dc/terms/subject> 13
rdfs:seeAlso 101
<http://purl.org/linguistics/gold/hypernym> 2
DBpedia2:precededBy 42
DBpedia2:author 93
DBpedia2:publisher 21
DBpedia2:books 101
foaf:isPrimaryTopicOf 1
item can be subject, object or predicate in a semantic graph,
with a reader-friendly example based on foaf ontology [31].
A few considerations are needed, however, when we start
discussing about the possibility to store information in a
semantic graph. In fact, a few critical points are present, and
have to be highlighted. First of all, as it is depicted in [32],
without regulations, the semantic graph is doomed to chaos,
i.e. to an unpredictable information taxonomy. The solution
to this issue is the ontological description of knowledge, that
consists in the formal definition of all the classes, relationships
and statements that can be present in the graph. Once the
programmers agree on the ontology, there is no uncertainty on
how the data is organized. All the information needed to query
the graph is stored in an OWL file, standing for Web Ontology
Language. OWL is, according to W3C, a “semantic markup
language for publishing and sharing ontologies”, and has been
widely used to define all s ort of o ntologies and vocabularies
(which are smaller ontologies): an interesting repository, in
this field of s tudy, is the L inked O pen Vocabularies website
which has been already presented in the Introduction.
A second critical point is connected to the dimension of
the graph, which can be considerable not only when we are
discussing about web-located knowledge bases like DBpedia,
or the Internet itself, but also in smaller applications exploiting
RDF and SPARQL. To make an example, let us perform the
query of Listing 1 to DBpedia.
As of September 2018 the output of the query, which is
a simple request to count all the classes that “The Lord of
the Rings” resource belongs to, is equal to 25. Clearly, far
from a naive and optimistic expectation of a few outputs
similar to :Book,:Novel and so on. Listing the actual
values consequently results in a 25-rows table that outlines
the evidence of the hidden complexity in the results analysis,
PREFIX rdf: <http://www.w3.org/1999/02/..>
PREFIX dbp: <http://dbpedia.org/resource/>
SELECT (count(?o) as ?count)
WHERE {
dbp:The_Lord_of_the_Rings rdf:type ?o
}
Listing 1. SPARQL query to all classes parent of the resource
dpb:The_Lord_of_the_Rings
even in simple situations. The complexity grows considerably
if we proceed querying on the following level (Listing 2).
PREFIX rdf: <http://www.w3.org/1999/02/..>
PREFIX dbp: <http://dbpedia.org/resource/>
SELECT ?p (count(?t) as ?count)
WHERE {
dbp:The_Lord_of_the_Rings ?p ?o.
?o rdf:type ?t
FILTER (?p != rdf:type)
}
Listing 2. SPARQL query to every link (except rdf:type) with
dpb:The_Lord_of_the_Rings as origin, and the destination’s class
The query available in Listing 2 with the variable ?count
outputs the number of links of type ?p outgoing from the
resource dbp:The_Lord_of_the_Rings, except from
rdf:type links, that can be viewed by performing the query
in Listing 1.
The direct outcome after running the queries in the Listings
1 and 2 is given by the possibility to observe the available
variability of results and to look for their meanings. The output
of those simple SPARQL queries highlights, for instance, that
the “Lord of the Rings” resource is individual of at least 25
classes which we expect to have a specific meaning and a
description of their own. Going further with the latter query,
moreover, the number of elements connected to the resource
is even more increasing, both as connectivity spread, and
in diversity of ontological classes involved. In general the
description of all those resources can be as pragmatic as
an algorithm, or philosophical, or mathematical. However, it
is clear that without the Semantic Web it would be hardly
achievable to obtain such a multi-layered description of a
resource, apart from using natural language. In fact, when
it comes to exploit the tools of Semantic Web, a frequent
feeling is that it is not possible to reuse previously available
data, because it would imply to understand completely all
the resources, all the classes, and all the ontologies that are
standing behind. According to [33], expressiveness, in this
situation, is a bottleneck for Semantic Web.
This is where visualization tools for the semantic graph
come to help: they provide a step by step approach to the
knowledge base that, together with filtering techniques, and
the possibility to see the contents, are useful to go through
the relevant concepts.
B. Possible visualizations
As we said in the previous Subsection, the most frequent
way to produce a view of a database is the tabular repre-
sentation. This is a possible solution also for queries made
in SPARQL language to RDF triple stores like Blazegraph,
Fuseki and Virtuoso. The view of a SPARQL SELECT is a
direct consequence of the number of variables concerned by
the inquire: i.e., the number of variables in the SELECT clause
is the same as the number of columns contained in the results.
To be more precise, to obtain the column number either (i) it
is necessary to count the variables queued after the SELECT
keyword, like in listings 1 and 2; or (ii), variables have to
be obtained from the WHERE clause, as in the SELECT *
WHERE {...} case.
The drawbacks with table views are, unfortunately, already
quite visible when the number of rows reaches as little as few
dozen entries. Aside from the fact that there is not a group
view of the overall query result, the table often is required
to contain more than one row for the same conceptual entity.
This happens for instance when a resource is connected to
another via more than one predicate, or when it is connected
to different objects, through the same predicate.
In such situations, the result table can contain not only
plenty of lines with the same meaning disturbing the overall
understanding of the query output, but also, as already said, a
high number of columns. Moreover, some entries in the table
can also be empty, as an effect of OPTIONAL statements
in the query. Detecting particular cases, in sparse and large
tables, becomes a time-consuming and error-prone task in
those situations. On the other hand, a few workarounds are
available in SPARQL language to crunch into a single line
the occurrence of multiple table lines for a single concept, but
they usually imply slowing down the performances, and have
the effect to concatenate the values into strings. That is, we
lose the possibility to check if they are represented as IRIs,
literals, or blank nodes.
The multi-table approach is a graph visualization technique
that tries to address the problem of having limited control
over the complete data table. Let’s consider a query selecting
all triples in the RDF store: SELECT *WHERE {?a ?b
?c}, and let’s suppose that in the store only 5 distinct
resources might correspond to the ?b variable. With this
background a full-table approach would return an n=3
column table, where nis the number of variables. Instead
a multi-table approach would outcome with 5 smaller tables,
one for each one of the ?b resources, each of them built up of
n1=2columns. An interesting work about the complexity
of translation from SPARQL to other languages, included table
view, was provided by Chebotko et al. in [34]: among all the
contributions, this paper perfectly shows the complexity of a
multi-table approach.
Finally, last but not least, the RDF knowledge base represen-
tation can be performed through a labeled graph visualization.
Although the RDF concept is defined for directed graphs,
in most of the cases the label is sufficient to get at view
time the direction of the connection. This allows the usage of
algorithms for undirected graphs. Nevertheless, the drawbacks
of this approach are also related to the knowledge base
dimension, as the understanding of contents is tightly bound
to the possibility of identify paths and node types easily and
effectively. In the next Subsection a few techniques for graph
drawing available in literature are presented.
C. Graph drawing algorithms
There is a complex relationship between the domain of
the semantic application, the tool that is being used, and
the algorithm that is implemented to visualize the graph. To
make an example, let’s consider a knowledge base in which
information about some people is stored. If the application
working on the knowledge base is not interested in literal
terms, the sight of the graph would be effectively simplified
and clearified by just removing all the links towards literal
terms, e.g. names, surnames and birth dates.
In other RDF triple stores more than one unique ontology
may have been used to define resources, exploiting for instance
simultaneously the foaf ontology and the Dublin-Core on-
tology (DC) [35]. If an application is interested only in the
foaf-related connections, and in a small part of the DC’s,
there would be no use in trying to represent everything.
A full description of all the algorithms available for graph
drawing is out of the scope of this paper. In this Section,
nevertheless, a brief overview of a few works available in
literature is given, before proceeding in Section IV to the
analysis of the tools.
A complete theoretical overview of the main algorithm logic
available to draw graphs is given by Kobourov in [36]. Spring
algorithms and their variations for instance are explained: they
usually aim to reproduce an aesthetically pleasant view, even
if their best performance is obtained in most of the cases when
the graph has less than 40 vertices. However, as it has been
said, the semantic graph is definitely a large g raph, or very
large, and for this reason it demands particular approaches
that imply multiple scale algorithms. Nodes organization is
not necessarily done on a plane: possible alternatives are to
dispose them on a sphere or other geometrical objects. In [37]
more than one plane is used, which can be a technique also
to represent the evolution of data over time. How to show in
an effective way dynamic evolution of contents in a graph is
also the topic of survey [38] by Beck et al.
IV. GRAPH VISUALIZATION TOOLS
This Section proposes a detailed analysis of the main tools
for the visualization of RDF knowledge bases and ontologies.
We focus on the tools providing a graph visualization of RDF
statements. The tools presented in this Section are reported in
alphabetical order.
A. CytoScape
Cytoscape [39] is a tool for network data integration, anal-
ysis and visualization. Support to Semantic Web technologies
is provided by a set of extensions hosted on CytoScape’s
App Store, such as General SPARQL, SemScape and Vital
AI Graph Visualization. General SPARQL allows to navigate
semantic web KBs through an extensible set of pre-defined
queries. The plugin is pre-configured to retrieve and visualize
data from public endpoints (e.g., Reactome, Uniprot, HGNC,
NCBI Taxonomy, Chembl). SemScape supports the interac-
tion with remote SPARQL endpoints by means of SPARQL
queries. In this way, CytoScape can be employed to visualize
the results of a query. Vital AI Graph Visualization is not
limited to semantic databases, but provides access also to SQL
and NoSQL databases as well as Apache Hadoop instances.
To the best of authors’ knowledge, this tool only allows the
visualization of data compatible with the BioPAX format.
B. Fenfire
Fenfire [40] was a tool for the visualization and editing
of RDF graphs aimed at an interactive exploration of the
graph. Authors face the problem of scalability by limiting
the exploration of the graph to one thing at a time. The
visualization in facts, diplays only one central node and
its surroundings. The central node, at the beginning of the
exploration is selected exploiting the foaf:primaryTopic
property (if present), otherwise is selected by the user. The
nodes surrounding the central one (named focus) are placed
on the plane according to a simple strategy: on the left, all the
nodes being subjects of the statements linking to the focus. On
the right, those being objects of the statements. Development
of Fenfire stopped in 2008.
C. Gephi
Gephi [41] is a very powerful tool designed to represent
not only semantic graphs, but every kind of graph or network.
Support to RDF graphs is provided by two external plugins,
VirtuosoImporter and SemanticWebImport (this one developed
by INRIA). Gephi is able to retrieve data from SPARQL
endpoints (through REST calls) as well as to load RDF files.
Gephi supports filtering the KB through SPARQL queries. The
look of the graph visualized by Gephi is fully customizable,
in terms of colors and layouts; moreover the tool supports
grouping similar nodes and this helps achieving better results
when dealing with very complex graphs. As regard exporting
the graph, Gephi is the tool that supports the highest number
of file formats for exporting the graph. Among these, it is
worth mentioning csv,pdf and svg.
In Figure 1 we can see a view of the graph that Gephi is able
to retrieve from DBpedia by using the SPARQL CONSTRUCT
available in Listing 3. The tool performs the representation
very quickly, and implements various possible algorithms to
build the graph. Unfortunately, as it can be seen, it is quite
difficult to get the overall idea of the composition. Although
there is the possibility to add the labels of nodes and edges,
the output is not reader-friendly, and the research in it is a
rather impossible task. A practical example can be observed
also in Figure 2, where we highlighted the nodes related to the
novel “The Black Cauldron” by L. Alexander. Eventually, a
number of statistical functions can be applied to the network,
like the Network Diameter, the Density and the Average Path
Lenght: the only problem is that they have, as for the Authors’
knowledge, very limited use when applied to a Semantic
Graph.
Fig. 1. Gephi [41] is capable to query DBpedia and show the result graph. The
Figure is the output of CONSTRUCT in Listing 3 (see Appendix). According
to Gephi’s logger, the triples represented in this graph are 6529.
Fig. 2. With Gephi [41] some nodes can be highlighted, to help the user
to go through the knowledge base. When the number of edges and nodes is
high, however, it’s not easy to outline the information. The nodes in red are
related to L. Alexander’s novel “The Black Cauldron”.
D. GLOW
Glow [42] is a visualization plugin for the ontology editor
Prot´
eg´
e. Force-directed, Node-link tree and Inverted radial tree
are the three layout algorithms provided by GLOW. The items
are arranged automatically with every layout, and cannot be
moved. The tool is able to represent a set of ontologies and
optionally their individuals. To the best of authors’ knowledge,
this tool is not developed anymore. No information about the
license could be found.
E. IsaViz
IsaViz [43] is a 2.5D tool for the visualization of RDF
graphs originally developed by E. Pietriga (INRIA) in collabo-
ration with Xerox Research Centre Europe. IsaViz, as the name
suggests, is based on GraphViz [44] and allows importing and
exporting from/to RDF/XML, Notation 3 and N-Triple files.
The result of the visualization can be also exported as a png or
svg file. In the Graph view it is possible to select resources
and access a textual list of properties (this view is named
Property Browser). A third view is named Radar and presents
an overview of the graph, since the graph view may contain
only a portion of it. Finally, it is worth mentioning the search
tool provided by IsaViz, whose results are highlighted one by
one in the graph view. Unfortunately, the last development
version of this tool dates back to 2007.
F. Jambalaya
Jambalaya [45] is a Prot´
eg´
e plugin for the visualization
of ontologies. Jambalaya is characterized by the integration
of the SHriMP (Simple Hierarchical Multi-Perspective) [46]
visualization technique, designed to improve the user experi-
ence in browsing, exploring, modelling and interacting with
complex information spaces. This technique, originally born
to help programmers understanding software, was applied
to Prot´
eg´
e to build a powerful visualization of classes and
relationships. The tool proposes a nested graph view and the
nested interchangeable views. Nesting is used to represent
the sub-class relationships among classes as well as the link
between classes and their instances (different colors allow to
distinguish between classes and instances). Jambalaya also
provide an easy way to search for items in the ontology.
Despite being an interesting tool developed with support
from the National Center for Biomedical Ontology (NCBO),
Jambalaya is not developed anymore.
G. LOD Live
LOD Live [47] is a web-based tool for the incremental nav-
igation of Linked Data available on a selected SPARQL End-
point (e.g., DBpedia). Endpoints can be configured through
a JSON map of their parameters, similarly to what happens
in Tarsier [37]. The purpose of this tool is to demonstrate
that the powerful Semantic Web standards are also easy to
understand; the aim is to foster the spread of Big Data.
Every resource drawn by LOD Live is surrounded by a set
of symbols representing different kinds of relationship (e.g.,
direct relations, group of direct relations, inverse relations and
group of inverse relations). The incremental navigation, joined
to the ability of the tool to group properties allows to draw a
very clean graph. No support for statistics or advanced filtering
(e.g., based on SPARQL) is provided. To the best of our
knowledge, directly exporting the graph is not possible. In
Figure 3 it is shown how LOD Live performs a similar task
as the one in Figure 2: exploring data is easier, but there is
no way to perform requests like the one in Listing 3.
Fig. 3. To use LOD Live [47] a resource must be fixed. Then, the knowledge
related to the resource can be expanded as shown. Like in Figure 2, the
example here is based also on L. Alexander’s novel “The Black Cauldron”.
H. Ontograf
Ontograf [48] is one of the visualization tools provided by
the famous ontology editor Prot´
eg´
e. The tool allows to build
a custom visualization of the ontologies loaded in Prot´
eg´
eby
iteratively enabling or disabling the desired classes. Ontograf
proposes a grid layout (with classes sorted in alphabetical
order), a spring layout and a (vertical or horizontal) tree layout.
Individuals of a class can be visualized in its tooltip, but this is
uncomfortable when dealing with a high number of assertional
statements. Ontograf allows to export the visualized graph as
a png, jpeg, gif or dot file. This tool exploits the layout library
provided by Jambalaya.
Fig. 4 shows a graph created with OntoGraf using the
DBpedia ontology. Classes work and written work were
initially selected. Then, a double click on the latter allowed
to expand it and visualize all the subclasses (solid blue line),
and all the classes linked to it by means of an object property
(dashed lines).
The last version of Ontograf dates back to April 2010, but is
still included in the last stable version of Prot´
eg´
e (the 5.2.0, as
of September 2018). The tool is useful to select and visualize
(a small number of) classes from the ontologies loaded in
Prot´
eg´
e and the existing relationships.
I. OntoSphere
OntoSphere [49] is one of the two tools (the other is Tar-
sier [37]) that proposes a three-dimensional visualization of the
graph. The rational behind OntoSphere is that exploiting a 3D
space it is possible to better arrange items. Moreover, the 3D
visualization is quite natural for humans and the exploration
can then be more intuitive. Colors allow to easily convey
information about the different nature of represented items.
OntoSphere is aimed at representing both terminological and
assertional statements. Four scene types are proposed to fulfill
different requirements. The RootFocus scene shows all the
concepts and their relationships on a sphere. The TreeFocus
scene draws the tree originating from a concept, while the
ConceptFocus scene proposes a view containing all the
Fig. 4. A portion of the DBpedia ontology visualized in Ontograf [48].
items linked to a concept. The tool is aimed at domain experts
dealing with the development and review of ontologies, as well
as novice users that wants to understand the represented data
and the links among concepts. OntoSphere is a standalone
applications, but can also be run inside Prot´
eg´
e and Eclipse.
The last version on the source code repository is dated 2008,
so the development stopped ten years ago.
J. OWLViz
OWLViz [50] is a plugin for Prot´
eg´
e that enables the
incremental visualization of the classes in the class hierarchy.
As the name suggests, this tool, like IsaViz, is based on
the famous library GraphViz developed by the AT&T and
allows exporting the visualized graph as png,jpeg and
svg. Through OWLViz is easy to visualize classes and is-a
relationships. OWLViz is not developed anymore, but is still
included in the last version of Prot´
eg´
e (September 2018).
K. Paged Graph Visualization
Paged Graph Visualization (PGV) [51] is a Java software
for the visualization of RDF graphs. It is based on [52], a
high performance RDF storage. With PGV, the exploration
starts from a point of interest and then incrementally includes
more data. Such point of interest can be selected interactively
from a list or using a complex SPARQL query. Then, it is
drawn in the center of the graph using the color green, and its
direct neighbors are shown as blue rectangles placed around
it. Literals on the other hand, are represented with the white
color. The user is able to explore nodes by double-clicking on
them: explored nodes are then displayed in green, while edges
connecting explored nodes are depicted in red.
Deligiannidis et al. [51] declare that the tool’s strength relies
in helping the user willing to explore data without knowing
the exact information and graph patterns he is looking for,
while in other situation a standard visualizer could be more
appropriate.
To the best of authors’ knowledge, this tool is not developed
anymore.
L. RelFinder
RelFinder [53] is a web tool developed using Adobe Flex
and can be tried using the web instance linked in the homepage
of the project (configured to access DBpedia). RelFinder
differs from the other tools proposed in this survey, since it is
aimed at visualizing all the paths connecting two resources. So,
its purpose is to answer a very specific question, rather than
providing a tool for the free exploration of the knowledge base.
The tool supports filtering to increase or reduce the number
of relationships shown simultaneously. It also implements a
smart drawing algorithm to reduce overlapping and the user
is allowed to move and pin items. To the best of authors’
knowledge, this tool is not actively developed but the online
instance is still available for tests on the DBpedia endpoint.
Fig. 5 reports an example of this application where all the
paths between two DBpedia resources, i.e, “JRR Tolkien” and
“The Lord of the Rings”, are shown. Fig. 6 shows the filtering
panel proposed by RelFinder to show/hide elements in the
visualization. Paths can be filtered by length, class of the RDF
terms, property and connectivity level.
M. Tarsier
Tarsier [37], is a tool developed by the authors of the
present paper. It is a software for the interactive exploration
of an RDF graph in a three-dimensional space, aimed at the
visualization of small and medium-sized knowledge bases.
The main contribution of the tool is the introduction of the
metaphor of semantic planes that group RDF terms sharing
a common concept. The purpose of the tool is threefold: 1)
Fig. 5. RelFinder [53] showing all the paths from “JRR Tolkien” to “The
Lord of the Rings”.
Fig. 6. RelFinder [53] filtering panel.
Tarsier can be used as a support for didactic (e.g., to help
newcomers to deal with Semantic Web technologies); 2) It is
useful to figure out the nature of a new KB for developers (i.e.,
activity known as “sensemaking” [54]) ; 3) It allows debugging
of semantic knowledge bases.
Tarsier retrieves data from SPARQL endpoints. The initial
knowledge base can be determined through a SPARQL Con-
truct query: this pre-filtering stage allows to efficiently interact
also with very large knowledge bases (e.g., DBpedia [55],
that contains more than 6.6M entities). Tarsier proposes a
classification of all the RDF terms among classes, resources,
blank nodes, literals, object and datatype properties. This
grouping is exploited by Tarsier’s web interface to provide
a set of controls for advanced filtering: through them, the user
is allowed to toggle visibility of items or to move them across
semantic planes.
An example of Tarsier is shown in Figg. 7 and 8. Tarsier
was set up to retrieve data from DBpedia, and in particular to
extract all the fantasy books published between 1900 and 2018
and their authors. While Fig. 7 shows the unfiltered knowledge
base, in Fig. 8 is shown one of the peculiarities of Tarsier: the
semantic planes. Two semantic planes were created over the
main knowledge base to extract respectively books and one
of the authors, i.e., Marion Zimmer Bradley. In this way, it is
easy to notice how this instance of the class foaf:Person
is linked with the rest of the graph.
Fig. 7. Tarsier [37] showing the graph of all the fantasy books published from
1900 to 2018 and their authors. This subgraph is retrieved from DBpedia.
Summarizing, Tarsier is a tool for the three-dimensional
multi-planar visualization of small/medium-sized knowledge
bases with advanced filtering mechanism based on the multiple
selection of RDF terms or SPARQL queries.
N. TGVizTab
This is yet another visualization plugin for the ontology
editor Prot´
eg´
e. TGVizTab [56] designed to be lightweight and
support both T-Boxes and A-Boxes visualization. TGVizTab
relies on TouchGraph, an open source Java environment aimed
at creating and navigating network graphs in an interactive
way. The tool supports exporting the graph in an XML file,
to be loaded in other TouchGraph applications. The graph is
drawn using the spring layout: similar nodes are drawn close
to each other. TGVizTab, like other tools (e.g., Fenfire), asks
the user to select a focal node among classes and instances to
generate the graph. Then, the user is able to further modify the
graph by right-clicking on the represented nodes: in this way
the so-called Node Menu is shown, containing four options
(i.e., expand, collapse, hide, view). Then TGVizTab allows to
incrementally build the desired visualization
O. VOWL
VOWL (Visual OWL) [57] is available as a web-based tool
(WebVOWL [58]), a plugin for Prot´
eg´
e (Prot´
eg´
eVOWL [59]),
a tool able to directly interact with Linked Data endpoints
Fig. 8. Tarsier [37] showing two semantic planes over the main knowledge
base: one showing books, the other (the topmost) showing the author Marion
Zimmer Bradley.
(LD-VOWL [60]), and as a visual query language tool
(QueryVOWL [61]). In this paper, we will refer to the web
based version, WebVOWL. As the name suggests, software
in the VOWL toolkit are designed to graphically represent
ontologies. They propose a force-directed graph layout. The
basic representation rules adpoted by VOWL consists in:
Classes are depicted using circles where the color de-
pends on the type: light blue for OWL classes, purple
for RDFS classes, dark blue for those imported by other
ontologies, gray for deprecated classes.
OWL object and datatype properties are represented with
black solid lines with, respectively, light blue and green
labels, while RDFS properties have purple labels.
Relationships subClassOf are depicted with a dashed
line.
The graph drawn by VOWL can be exported as an svg
image or as a json file. A click on a node or edge allows
visualizing the associated metadata and statistics. Statistics
also report the number of individuals of the selected class, but
unfortunately this is the only information about individual that
is possible to obtain using VOWL. As regards filtering, VOWL
provides a basic support to filters that allows to show/hide
object/datatype properties, solitary classes, class disjointness
and set operators.
VOWL is actively developed and an online instance is
available. As the tool is designed for ontologies, importing the
output of the CONSTRUCT in Listing 3 results in representing
only the two rdf:type relationships. The other tools are still
being developed and at the moment do not allow to perform
a customized request to DBpedia.
Fig. 9. Overview of the DBpedia ontology in WebVOWL2 [58].
Fig. 10. WebVOWL2 [58]: Close-up on two of the classes defined in the
DBpedia ontology.
V. SUMMARY
Table III summarizes the main features of the analyzed
software. Columns of the table are:
Software – reports the name of the software;
T-Boxes – this column tells if the tool supports the
visualization of terminological statements;
A-Boxes – this column shows if the tool supports the
visualization of assertional statements (and can then be
used to explore a knowledge base, rather than just on-
tologies);
Statistics – a boolean field showing if the tool provides
or not statistics on the visualized data;
Filtering – filtering allows to show/hide elements in the
visualization according to a set of user-defined criteria.
Filtering can be implemented in very different ways (e.g.,
SPARQL queries, or UI controls to select classes, just to
name a few). This column indicates whether the related
tool provides at least one filtering mechanism.
Editing – This paper surveys visualization tools for
semantic data, but some of them also offer editing func-
tionalities. This column states whether or not the related
tool supports the manipulation of the ontology/knowledge
base;
Standalone – Many of the surveyed tools were born as
plugins for the ontology editor Prot´
eg´
e. Other can be run
as standalone software. This column tells if the related
software is embedded in other tools or is a standalone
application.
Plugin – Not all the presented tools were born to visualize
semantic knowledge bases. Then, some of them need
additional plugins to achieve this task.
Domain – This column contains the specific domain (if
any) where the related application can be applied.
Reference – This column reports the reference number
of the paper(s) describing the tool.
Table IV summarizes information about the entities that
started the development of the tool, the license and the current
status of the project.
VI. CONCLUSION
This paper presented an analysis on the current status of
the tools for the visualization of ontologies and knowledge
bases exploiting a graph representation. Results of this study
contrast with the wide spread of Semantic Web technologies:
in fact, among the 15 software surveyed by the authors, only
5 are still active. It is also worth noting that 6 of them are
available as visualization plugins for the popular ontology
editor Prot´
eg´
e. Advanced filtering through SPARQL queries
is provided, to the best of our knowledge, only by Gephi and
Tarsier. Future work will consist in the analysis of other tools
exploiting different representations with a detailed set of use
cases for their evaluation.
APPENDIX
In Listing 3 we report the SPARQL CONSTRUCT query
adopted in the practical examples shown in this Paper.
ACKNOWLEDGEMENTS
The work presented in this paper is being developed at the
Advanced Research Center on Electronic Systems Ercole De
Castro (ARCES), University of Bologna, 40125 Bologna, Italy.
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PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX xsd: <http://www.w3.org/2001/...>
PREFIX rdfs: <http://www.w3.org/2000/...>
PREFIX rdf: <http://www.w3.org/1999/...>
PREFIX : <http://dbpedia.org/resource/>
PREFIX dbpo:<http://dbpedia.org/ontology/>
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FILTER langMatches(lang(?label), "EN")
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OPTIONAL {
?book dbpo:releaseDate ?date .
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TABLE III
SUMMARY OF THE FEATURES OF THE TOOLS FOR THE VISUALIZATION OF SEMANTIC KNOWLEDGE BASES.
LEGEND:=YES,=NO,=PARTIAL,=MULTIPLE OPTIONS AVAILABLE,?=UNKNOWN,=NOT APPLICABLE
Software T-Boxes A-Boxes Statistics Filtering Editing Standalone Plugin Domain Reference
CytoScape    General SPARQL,
SemScape,
Vital AI
Biology [39]
Fenfire   General [40]
Gephi     SemanticWebImport,
VirtuosoImporter
General [41]
Glow    General [42]
IsaViz    General [43]
Jambalaya    General [45]
LOD Live     General [47]
Ontograf    General [48]
OntoSphere    General [49]
OWLViz    General [50]
PGV    General [51]
RelFinder    General [53]
Tarsier    General [37]
TGVizTab    General [56]
VOWL    General [57]–[59]
TABLE IV
INFORMATION ABOUT DEVELOPERS,DEVELOPMENT AND LICENSES.
LEGEND:=YES,=NO,?=UNKNOWN
Software Developed by License Active Reference
CytoScape CytoScape Consortium GPL [39]
Fenfire University of Jyw¨
askyl¨
a and Digital Enterprise Research Institute of the National
University of Galway
GPL [40]
Gephi Gephi Consortium GPL [41]
Glow Erasmus University Rotterdam ?[42]
IsaViz INRIA in collaboration with Xerox Research Centre Europe GPL [43]
Jambalaya Chisel Lab (University of Victoria) Individual [45]
LOD Live lodlive.it MIT [47]
Ontograf Stanford Center for Biomedical Informatics Research LGPL [48]
OntoSphere Politecnico di Torino LGPL [49]
OWLViz University of Manchester LGPL [50]
PGV LSDIS Lab and Computer Science (University of Georgia), Kno.e.sis Center (Wright
State University)
?[51]
RelFinder Visualization and Interactive Systems (University of Stuttgart), Agile Knowledge Engi-
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Design (University of Duisburg-Essen)
GPL [53]
Tarsier Advanced Research Center on Electronic Systems (University of Bologna) GPL [37]
TGVizTab IAM Group (University of Southampton) GPL [56]
VOWL Visualization and Interactive Systems (University of Stuttgart), Alexandru Ioan Cuza
University
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Questionnaires on health-related quality of life (HRQoL) play a crucial role in managing patients by revealing insights into physical, psychological, lifestyle, and social factors affecting well-being. A methodological aspect that has not been adequately explored yet, and is of considerable potential, is causal discovery. This study explored causal discovery techniques within HRQoL, assessed various considerations for reliable estimation, and proposed means for interpreting outcomes. Five causal structure learning algorithms were employed to examine different aspects in structure estimation based on simulated data derived from HRQoL-related directed acyclic graphs. The performance of the algorithms was assessed based on various measures related to the differences between the true and estimated structures. Moreover, the Resource Description Framework was adopted to represent the responses to the HRQoL questionnaires and the detected cause–effect relationships among the questions, resulting in semantic knowledge graphs which are structured representations of interconnected information. It was found that the structure estimation was impacted negatively by the structure’s complexity and favorably by increasing the sample size. The performance of the algorithms over increasing sample size exhibited a similar pattern, with distinct differences being observed for small samples. This study illustrates the dynamics of causal discovery in HRQoL-related research, highlights aspects that should be addressed in estimation, and fosters the shareability and interoperability of the output based on globally established standards. Thus, it provides critical insights in this context, further promoting the critical role of HRQoL questionnaires in advancing patient-centered care and management.
... Games with a purpose [9] are often utilized to curate KGs, for example, with crossword puzzles [131], rating [109] or question answering [40]. To let participants see and inspect the modeled KG, a common method is graph visualization and browsing [12]. ...
Preprint
This paper presents a retrospective overview of a decade of research in our department towards self-organizing personal knowledge assistants in evolving corporate memories. Our research is typically inspired by real-world problems and often conducted in interdisciplinary collaborations with research and industry partners. We summarize past experiments and results comprising topics like various ways of knowledge graph construction in corporate and personal settings, Managed Forgetting and (Self-organizing) Context Spaces as a novel approach to Personal Information Management (PIM) and knowledge work support. Past results are complemented by an overview of related work and some of our latest findings not published so far. Last, we give an overview of our related industry use cases including a detailed look into CoMem, a Corporate Memory based on our presented research already in productive use and providing challenges for further research. Many contributions are only first steps in new directions with still a lot of untapped potential, especially with regard to further increasing the automation in PIM and knowledge work support.
... Elements of a knowledge graph are usually explored via graph-based, textbased, or mixed interfaces. The authors in [38] present a survey of tools designed to visualise the content of KGs. These tools leverage the intrinsic characteristics of the RDF model; therefore, they are explicitly designed to explore a whole KG and its structure. ...
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... Moreover, ref. [26] surveys and categorizes OLAP approaches that leverage semantic web technologies according to several criteria, including materialization, transformations and extensibility. Finally, there are also available surveys [32,33] that describe visualization approaches for RDF KGs and surveys for summarization for semantic RDF graphs, e.g., see [34]. ...
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... Information visualization, through the use of visual representations of abstract data, reinforces human cognition to support the discovery of unstructured insights only limited by human imagination and creativity, making it a suitable approach to communicate the knowledge described by RDF datasets. In particular, we observe an increasing interest in using visual and interactive techniques to explore LOD resources via multiple criteria and levels of abstraction by the Semantic Web community to accomplish three main goals: (i) to explore the relevant concepts of an application domain via ontology representation; (ii) to inspect RDF graphs (e.g., "for debugging triples") [1]; and (iii) to analyze the instances based on their types/classes. ...
... A thorough survey on LOD visualization is beyond the scope of this article, so we refer the interested reader to the surveys by Antoniazzi and Viola (2018), , Dadzie and Rowe (2011), and to the set of articles organized by Dadzie and Pietriga (2016). As suggested by the number of surveys on the subject we find in the literature, there are various visualization approaches to assist the exploration of linked data. ...
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... Concerning the visual analysis of KGs, multiple tools have been developed throughout the years. Recent research efforts [1,6] focused on listing, analyzing, and comparing existing Linked Data (LD) visualization tools able to deal both with KG schema and data. The majority of the available tools rely on a graph-based visualization and present several commonalities with respect to the provided functionalities and input mode. ...
Chapter
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Chapter
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Visualizations of ontologies, in particular graph visualizations in the form of node-link diagrams, are often used to support ontology development, exploration, verification, and sensemaking. With growing size and complexity of ontology graph visualizations, their represented information tend to become hard to comprehend due to visual clutter and information overload. We present a new approach of semantic zooming for ontology graph visualizations that abstracts and simplifies the underlying graph structure. It separates the comprised information into three layers with discrete levels of detail. The approach is applied to a force-directed graph layout using the VOWL notation. The mental map is preserved by using smart expanding and ordering of elements in the layout. Navigation and sensemaking are supported by local and global exploration methods, halo visualization, and smooth zooming. The results of a user study confirm an increase in readability, visual clarity, and information clarity of ontology graph visualizations enhanced with our semantic zooming approach.
Conference Paper
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This is the third edition of the premier professional reference on the subject of data mining, expanding and updating the previous market leading edition. This was the first (and is still the best and most popular) of its kind. Combines sound theory with truly practical applications to prepare students for real-world challenges in data mining. Like the first and second editions, Data Mining: Concepts and Techniques, 3rd Edition equips professionals with a sound understanding of data mining principles and teaches proven methods for knowledge discovery in large corporate databases. The first and second editions also established itself as the market leader for courses in data mining, data analytics, and knowledge discovery. Revisions incorporate input from instructors, changes in the field, and new and important topics such as data warehouse and data cube technology, mining stream data, mining social networks, and mining spatial, multimedia and other complex data. This book begins with a conceptual introduction followed by a comprehensive and state-of-the-art coverage of concepts and techniques. Each chapter is a stand-alone guide to a critical topic, presenting proven algorithms and sound implementations ready to be used directly or with strategic modification against live data. Wherever possible, the authors raise and answer questions of utility, feasibility, optimization, and scalability. relational data. -- A comprehensive, practical look at the concepts and techniques you need to get the most out of real business data. -- Updates that incorporate input from readers, changes in the field, and more material on statistics and machine learning, -- Scores of algorithms and implementation examples, all in easily understood pseudo-code and suitable for use in real-world, large-scale data mining projects. -- Complete classroom support for instructors as well as bonus content available at the companion website. A comprehensive and practical look at the concepts and techniques you need in the area of data mining and knowledge discovery.