=Paper=
{{Paper
|id=None
|storemode=property
|title=Using Contexts in Ontology Structural Change Analysis
|pdfUrl=https://ceur-ws.org/Vol-626/demo.pdf
|volume=Vol-626
|dblpUrl=https://dblp.org/rec/conf/ekaw/ErmolayevCKJM10
}}
==Using Contexts in Ontology Structural Change Analysis==
https://ceur-ws.org/Vol-626/demo.pdf
Using Contexts in Ontology Structural Change Analysis
Vadim Ermolayev1, Anton Copylov2, Natalya Keberle1,
Eyck Jentzsch3, Wolf-Ekkehard Matzke3
1
Zaporozhye National University, Zhukovskogo st. 66 69063 Zaporozhye Ukraine
vadim@ermolayev.com, nkeberle@gmail.com
2
Metrotech IT, 46 Gryaznova st. Zaporozhye Ukraine
anton.copylov@gmail.com
3
Cadence Design Systems GmbH, Mozartstr 2 D.85622 Feldkirchen Germany
jentzsch@cadence.com, wolf@cadence.com
Abstract. This demonstration paper presents the Ontology Difference
Visualizer software tool. This tool helps making a certain step forward in
improving the productivity and the accuracy of ontology engineering work. It
provides a visualization of the structural difference between the two compared
ontology schemas in the extended UML class diagram notation. Such
visualization is built based on the comparison of the ontology code in OWL-DL
using the PROMPTDiff algorithm. Having the difference between the
ontologies visualized we allow checking at the model level how the intended
modification of the source ontology has been implemented in the target
ontology. The particular focus of this demonstration is the use of the contexts –
the structural partitions of an ontology. Using contexts allows making the task
of the change analysis more focused and less complex. For that the
functionality is provided for concentrating on the semantic neighborhoods of
the analyzed concepts with respect to different requirements or different owners
within the team of ontology engineers.
Keywords: ontology, structural difference, ontology context, visualization.
1 Introduction
Ontology engineering is the discipline that, among the other important objectives, is
concerned about the development of the methods and tools for building ontologies so
as to fulfill the requirements of the target users about the common sense or a target
subject domain. As the analogy to the other engineering domains suggests, industrial
engineers will seek for and accept a methodology that is well defined and based on
the use of standardized working patterns. However the development of ontologies is
still more a craft work or a non-trivial mental exercise than a rigorous and
standardized engineering process.
An industrially strong engineering methodology must contain a well defined and
rigorous verification workflow – to check if the requirements have been correctly and
fully implemented in the developed artifact. Such a flow will only be efficient if
supported by a tool that releases an engineer from the burden of routine and effort
consuming operations. For instance, if an iterative ontology development process is in
operation, there is a need to present the differences between the source and the target
version of the ontology. The difference has to be presented in a form that could be
easily comprehended and analyzed by the verification engineer. His task then is to
compare the generated difference report with the requirements to the target ontology
version and to judge about the correctness and completeness of the implementation.
Verification becomes even more important when the artifact is developed
collaboratively by several engineers or even distributed teams working on its different
blocks. In this case the result needs to trace the errors to the proper context of the
engineer who owns the development of the fragment in focus.
The objective of this paper is to demonstrate the tool for helping verifying
ontology engineering work – Ontology Difference Visualizer (ODV). The proof of
concept prototype of ODV has been developed to support the verification steps of the
Shaker Modeling Methodology for ontology refinement [1], [2] in the PSI project 1 .
The design choices for the prototype are explained based on the review of the related
work in Section 2. ODV generates the report about the structural difference in the pair
of ontologies and visualizes this difference using the extended notation of UML class
diagrams as presented in Section 3. ODV allows analyzing the difference by
appropriate parts that are called ontological contexts as presented in Section 4. The
operational context model of ODV is based on the context model of PSI Upper-Level
Ontology [1]. Section 5 presents the ODV demonstration that uses the pair of versions
of the PSI Core Time ontology – v.2.2 and v.2.3. This pair of ontology versions has
been used in one of our tool evaluation and validation experiments. Finally, the paper
is concluded and the plans for the future work are outlined in Section 6.
2 Related Work
The central part of the presented work is the visualization of ontology changes.
Therefore, the related work to be analyzed is the results in ontology visualization with
the emphasis on the visualization of the structural changes in ontologies.
Methods and tools for ontology visualization (please refer to [3] for a detailed
review) are classified by the basic representation style into the following categories:
indented list (Protégé 2 , OntoEdit [4]); node-link (OntoViz 3 , OWLViz 4 , OntoSphere
[5]); zoomable view (Jambalaya [6], CropCircles [7]); space filling (treemap
visualization of gene ontologies [8]); focus plus context or distortion (hyperbolic view
in TGVizTab [9]). Currently the tools for ontology development more often use a 2D
visualization metaphor. Examples are OWLViz, TGVizTab, Jambalaya plug-ins for
Protégé. 3D visualization approach is also investigated in, for example, [10],
OntoSphere [5]. OntoSphere is a Protege plug-in using 3D visualization metaphor and
interaction in order to intelligently navigate through the dense information space. In
1 Performance Simulation Initiative (PSI) is the internal R&D project of Cadence Design
Systems GmbH.
2 Protégé Project. Stanford University, http://protege.stanford.edu
3 OntoViz plug-in for Protégé, http://protegewiki.stanford.edu/wiki/OntoViz
4 OWLViz plug-in for Protégé, http://protegewiki.stanford.edu/wiki/OWLViz
the prototype presented in [10] the sphere-packing technique is used instead of 2D
circle-filling (used in CropCircles [7]) in order to combine the 3D navigation
(rotation, semantic zoom) with the fine tuning of the level of details.
Standardization efforts in visualizing ontologies are mainly within OMG [11].
OMG elaborates the UML meta-model for the representation of ontologies encoded
among others in RDF and OWL. Since definition of UML Ontology Definition
Metamodel for OWL DL in [12], UML-based visualization of ontologies is used both
in commercial tools like TopBraid 5 Composer™, Sandpiper 6 Software Visual
Ontology Modeler™ and in freely available tools, e.g. in OWLGrEd [13].
Our ODV presented in this paper uses UML-based notation for representing the
visualizations of structural changes in ontologies. The basic notation has been chosen
because of the standardization efforts of OMG and the use of UML-based
visualizations of ontologies in some commercial tools. One more argument in favor of
the UML-based notation was that it is widely accepted across disciplines as a visual
language for modeling and design. Therefore, its use helps decreasing the ramp-up
efforts of both the ontology engineers and the subject experts to start understanding
this visual ontology representation. We have proposed the extension of the UML class
diagram notation that is presented in Section 3.
Unfortunately there are not many approaches and tools for visualizing structural
differences in ontologies. One relevant approach implemented in the software tool is
the PROMPT-Viz 7 Protégé plug-in [14], relying on PROMPTdiff [15] in calculating
structural difference between ontologies. The visualization combines hierarchically
embedded rectangles – nested treemaps – with a zoomable user interface. The
treemap notation can only be effectively used for hierarchical structures in ontologies,
and can not be easily extended. Another example is the visualization of differences in
indented lists in OWLDiff 8 .
With respect to computing structural differences in ontologies several research
results, comprising algorithms and software prototypes, need to be mentioned.
However we omit a detailed discussion of this aspect here as the focus of this paper is
visualization and refer to our technical report [16] for a detailed comparative analysis
of these algorithms and software tools. The ODV uses the PromptDiff algorithm [15]
for computing structural difference.
3 Extended UML Notation for Structural Change Visualization
In the developed extension of the UML class diagram notation for structural change
visualization, every change is presented as a set of atomic sub-changes of two types –
added or removed elements. The added elements are marked green and the removed
– red. In the cases of compound changes the diagram contains the minimal
information about such a change and also comprises every element required for the
visualization of the change.
5 TopQuadrant TopBraid Composer, http://www.topquadrant.com/products/TB_Composer.html
6 Sandpiper Software Visual Ontology Modeler, http://www.sandsoft.com/products.html
7 PROMPT-Viz plug-in for Protégé, http://protegewiki.stanford.edu/wiki/PromptViz
8 OWLDiff plug-in for Protégé, http://protegewiki.stanford.edu/wiki/OWLDiff
OWL classes are represented by UML classes. The removed OWL classes are
rendered with red border and class name. The added OWL classes – with green border
and class name. If a class is renamed both the old name (red) and the new name
(green) appear in the class box (Fig. 1a).
OWL generalization changes are visualized as colored UML generalizations (Fig.
1b). Added or removed generalizations to OWL: Thing class are not displayed.
OWL datatype properties are presented as UML class attributes. The range of a
property forms the type of the corresponding attribute, the property name determines
the name of the corresponding attribute and the domain determines the class-holder of
the attribute. Added datatype properties are marked green, removed datatype
properties are marked red. Renamed attributes are visualized as the combination of
the added attribute with the new name and the removed attribute with the old name to
provide the complete information about the change (Fig. 1c). So far the notation does
not allow rendering all the possible changes in datatype properties – for example the
change of the type of an attribute (OWL property range). The refinement is planned
for the future work.
removed concept added concept renamed concept
Concept A Concept B Concept A Concept A SyntheticClass
Concept B (formed by some sorts
of restrictions)
(a) Concept-level changes property
removed generalization added generalization
Concept A Concept B Concept A
Concept B Concept C Concept D
(b) Generalization changes
(e) Changes in complex constraints
Concept A 0..1
removedProperty: type Concept A 0…* objectProperty 0..1 Concept B
addedProperty: type {symmetric}
{transitive}
OLD: property: type
changedProperty (f) Changes in cardinality restrictions and object property
NEW: property: type semantics
Concept A
(c) Datatype property changes
addedObjectProperty
{disjoint}
Concept A removedObjectProperty Concept B Concept A Concept B {overlapping}
oldPropertyName Concept B Concept C
newPropertyName
Union
(d) Object property changes (g) Changes in Boolean (h) Changes in generalization
combinations constraints
Legend: The following denotation for colors has been introduced to provide the readability of the diagrams in the black and white mode.
Text labels: strikedthrough labels correspond to red; underlined labels correspond to green.
Lines and borders: dashed lines ( ) correspond to red; dotted lines ( ) correspond to green
Fig. 1. The notation for ontology structural change visualization (extension of UML).
Object properties are presented as UML associations. When a property doesn't
have the inverse property its name becomes the association name. When a property
has the inverse property, their names are used as association roles. Deleted object
properties are visualized as associations marked red while added ones are marked
green. Renamed properties are visualized as associations with two names – the old
name marked red and the new name marked green (Fig. 1d).
Domain and range restriction changes are rendered as added or removed
associations. Unnamed classes formed by complex restriction statements are
represented by synthetic classes. In such cases only the changed parts of a synthetic
class are marked with color. Nevertheless, the whole synthetic class must be shown to
ensure the completeness of the change diagram (Fig. 1e).
Changes to cardinality restrictions are represented as cardinalities of associations
marked with corresponding color (Fig. 1f). The changes in functional, inverse
functional, symmetric, and transitive statements for object properties are represented
as the semantics of associations, marked green for additions and red for deletions
(Fig. 1f).
Enumeration, union, or intersection axioms are rendered as quads containing the
set of internal UML elements. Each quad consists of the name of the logical operation
and the set of operands (classes or individuals). Changed elements in the quad are
marked green (added) or red (removed). The unchanged elements are also shown
(Fig. 1g).
Generalization constraints are displayed as per the UML standard. The removed
constraints are rendered red and the added ones are green (Fig. 1h).
The presented notation for ontology change has been deliberately restricted to
render the structural changes in ontology schemas (TBox). The reason is that the
software tool for analyzing differences (ODV) has been developed to support the
particular phase of Ontology Refinement and Validation in the Shaker Modeling
methodology for ontology refinement. Structural changes where the instances of
ontologies are involved are analyzed within a different methodology phase – ontology
ABox Migration (Fig. 4). This analysis is supported by a different software tool we
developed [23].
4 Context Model and ODV Functionality
ODV allows analyzing the difference between the compared ontologies by
appropriate parts that are called ontological or structural contexts. The formal model
for representing contexts is the one of the PSI Upper-Level Ontology [17]. Here the
context model and its implementation and use in the ODV are briefly presented.
As only the structural part of the context model is relevant for ODV (Fig. 2, dark
grey concepts), the process related part of the upper-level model is not in use. The
relevant part of the formal model could be interpreted as follows.
A Context 9 of an entity (that has the context) is the selection of related things that
facilitate interpreting, using, or performing the entity having this context in a
pragmatic way. For denoting a Context it is therefore required to answer:
(i) The context of what is specified? A Context could be either of a Process or of
an Object. For ODV the context of a Process is not relevant while the Objects for
ODV are the concepts of the analyzed ontologies. So, we are interested in the contexts
of ontology concepts.
(ii) What is relevant for the inclusion in the context? An instance of a Context
may aggregate the instances of a Process or of an Object as relevant referential
9 http://isrg.kit.znu.edu.ua/ontodocwiki/index.php/Context
constituents. For ODV only Objects are relevant constituents where the instances of
an Object would be the concepts of the analyzed ontologies together with all their
properties.
SUMO: Entity DOLCE: Perdurant DOLCE: Endurant
temporalParthood
PSI-ULO: Holon
PSI-ULO: Event structuralParthood
0..*
1..*
0..* PSI-ULO: Context
+contains PSI-ULO: Environment
+of
+isRelevantTo +contains
+isRelevantTo +has
1..* 1..*
0..* +contains +of
1..* 0..1 0..* 1..*
+belongsTo
PSI-ULO: Process
+has +of PSI-ULO: Object
1..* 0..* 0..1 0..1 1..*
1..*
+has +managedBy +isFocusOf
+of +has
+worksIn
PSI-ULO: MaterialObject
0..*
0..*
PSI-ULO: Agent
+manages
Legend: (mA…MA), (mB…MB) are the multiplicities denoting the (instance) cardinality of the relationship:
(m,M)A specifies how many (minimally, Maximally) instances of A may be related to the ONE SPECIFIC instance of B;
(m,M)B specifies how many (minimally, Maximally) instances of B may be related to the ONE SPECIFIC instance of A.
DOLCE is the foundational ontology of the WonderWeb ontology library [18]; SUMO is the Suggested Upper Merged
Ontology [19]; PSI-ULO is the PSI Upper-Level Ontology [1]
Fig. 2: The upper-level context model [17] used in ODV.
(iii) Who uses the Context? A Context is used by an Agent to define the current
working focus and determine working priorities. For ODV the instance of an Agent
will be the user (the ontology engineer) who is the owner of the concept whose
structural context is described.
Fig. 3 presents the desktop of the ODV. The composition of a context of a concept
(0), as implemented in the ODV, could be formed by specifying the radius of the
neighborhood of this concept (1). Further it could be fine-tuned by manual inclusion
or exclusion of the concepts (2), object properties (3), subsumption relationships (4).
The analyzed ontological context may be placed on the wafer of the source (old)
ontology by toggling the “show old” mode in the Tools menu. The context may be
also altered by considering or filtering out the concepts belonging to the imported
ontology modules (5). Finally the “owner” filter may be employed for concentrating
on the changes that have been introduced by a particular ontology engineer in the
team (6).
The ODV implementation allows also editing and saving the layout of the
visualized structural difference in the project file (7). Such a layout saves all the
context settings and therefore allows personalized representations for different users.
The reported release of the ODV proof of concept software prototype has been
implemented in Java as a plug-in to the Cadence ProjectNavigator software prototype.
ODV uses OWL API 2 and therefore is capable of processing OWL ontologies coded
in OWL DL. OWL DL has been used in the ontologies that have been analyzed in
ODV evaluation experiments.
5 ODV Demonstration
For the demonstration of the ODV the pair of the PSI Core Time ontology versions
(2.2 and 2.3) has been selected. The reasons for the selection of this particular pair of
ontologies are: (i) the ontologies are small enough for being effectively demonstrated;
(ii) structural changes were substantial and the types of changes in this pair of
ontology versions cover almost all the spectrum of the change notation; and (iii) the
ontology engineering work on the refinement of the Time ontology has been
documented in line with the phases of the ontology engineering methodology [2] –
this documentation may be used as a back-up demonstration material.
(1)
(7)
(0)
(2)
(3)
(4)
(5)
(6)
Fig. 3: The ODV desktop. Visualized is the structural difference between the PSI Time Core
ontologies v.2.2 and v.2.3.
The primary reason for the change requirements to the Time ontology v.2.2 was
that the underlying minimal model of time [20] was not capable of meeting the
requirements for the development of the design project scheduling component for the
Cadence ProjectNavigator [21]. Therefore it has been decided that the formal model
of time is upgraded to the time crisp model [20] and the ontology will be refined so as
to provide the descriptive models for: (i) the phases of time intervals; (ii) periods – the
finite time intervals associated to the particular repetitions of events; and (iii) the sets
of periods – the collections of periods describing the part of the time line
corresponding to all the repetitions of the event. These requirements have been
implemented in the Time ontology v.2.3 10 .
Following the Shaker Modeling Methodology, the team comprising two ontology
engineers and two subject experts: have specified the requirements; have refined the
formal model of time; have proposed the UML model of the proposed solution; have
discussed this model, refined it and agreed on the release candidate; have
implemented the ontology in OWL-DL based on the agreed model. After performing
these development steps the changes in the ontology have been verified using the
ODV (Fig. 4). The first iteration of the change analysis revealed that though all the
requirements have been accounted for in the proposed UML model, the OWL-DL
ontology code did not implement all the required changes. These errors have been
easily detected using context filtering. The knowledge engineer who was the owner of
the context containing the error has been tasked to provide the correction. The next
iteration of the change analyses revealed no errors.
Formal Upper Commonsense
User Framework Ontology Alignment
Evaluation Refinement Refinement
r
Taxonomy Bridging
c Refinement
Domain
Require- Ontology
ments Refinement ABox Migration
r
and
Validation
m r
+
Domain-Level
Ontology (PSI
Domain-Level
Time v.2.2) r r
Ontology Ontology (PSI Visualization
Difference Time v.2.3) of Structural
Visualizer Difference
c
Fig. 4. The use of ODV to support the Shaker Modeling Methodology for ontology refinement.
The methodology is presented using the ISO/IEC 24744 notation [22].
As it could be seen in Fig. 4, the ODV is the tool that supports the verification
steps of the ontology refinement phases of the methodology. It computes and
visualizes the structural difference between the older version of the ontology that has
been developed before (in the previous methodology iteration) and the newer version
of the ontology. The visualization diagram can be stored as an image and further used
as a report for documenting the process of ontology engineering. The verification
engineer manually compares the requirements produced in the user evaluation phase
to the generated difference diagram to check if all the requirements have been
properly implemented. We have observed in the evaluation experiments that the
contextualization features of the ODV noticeably increase the performance of the
validation engineer in executing this important operation.
6 Concluding Remarks and Outlook
The paper supports the demonstration of the ODV software tool. Emphasis has been
put on the explanation of how this tool uses ontological contexts for making the
10 http://isrg.kit.znu.edu.ua/ontodocwiki/index.php/PSI_Core_Time_ontology
collaborative work of ontology engineers more productive – in particular in the
verification step of ontology refinement. The ODV computes the structural difference
between the pair of ontologies and renders this difference using the presented
extension of the UML class diagram notation. The layout and the rendered ontological
context may be altered and saved in a project file thus enabling personalized views on
the parts of the ontologies to be verified.
For computing structural differences the ODV uses the PromptDiff fixpoint
algorithm mainly because of its modularity and extendibility. For the future it is
planned that several heuristic matches will be developed as extensions. At the
moment the ODV is a single user prototype that uses local file system as the ontology
repository. As the tool is thought as an instrument for collaborative work in a
distributed team it will be further developed to enable multiuser work with a
centralized triple store. Furthermore, the ODV may reveal its full potential as a
verification and validation instrument only as a component of an ontology model
(schema) editor. The development of such an editor and the integration of the
upcoming revisions of ODV into it are also the plans for our future work.
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