LITERATURE SURVEY ON

ONTOLOGY DEVELOPMENT

USING PROTÉGÉ

DAVID TUMINI OGOLO

20214129

DEPARTMENT OF SOFTWARE

ENGINEERING

[email protected]
INTRODUCTION

The Semantic Web, sometimes known as Web 3.0, is an extension of the World Wide
Web through standards set by the World Wide Web Consortium (W3C). The goal of the Semantic
Web is to make Internet data machine-readable. The vision of the Semantic Web introduces the
next generation of the Web by establishing a layer of machine-understandable data e.g. for
software agents, sophisticated search engines and web services. Semantic web identifies a set of
technologies, tools, and standard which form the basic building blocks of an infrastructure to
support the vision of the web associated with meaning.
An ontology is a formal description of knowledge as a set of concepts within a domain and the
relationships that hold between them. To enable such a description, we need to formally specify
components such as individuals (instances of objects), classes, attributes and relations as well as
restrictions, rules and axioms. As a result, ontologies do not only introduce a sharable and reusable
knowledge representation but can also add new knowledge about the domain.
Ontology is the main term in the semantic web. Protégé tool is the most popular and widely used
tool for ontology development. Protégé is a free, open source ontology editor and knowledge-base
framework. The Protégé platform supports two main ways of modeling ontologies via the Protégé-
Frames and Protégé-OWL editors. Protégé ontologies can be exported into a variety of formats
including RDF, RDFS, OWL, and XML Schema

LITERATURE REVIEW

Developing University Ontology using protégé OWL Tool: Process and Reasoning.
Developing Model for library Ontology Using Protégé Tool: Process, Reasoning and
Visualization

Naveen et al (2011) and Usman et al (2019) share the same view on the development and
application of ontologies. They believe that ontologies are gradually becoming the corner stone of
the semantic web because ontologies aim at capturing domain knowledge ledger in a generic way
and also provide a commonly agreed understanding of the domain. Using protégé 4.1 beta versions
they were able to develop an ontology for the R.G.P.V. University, Bhopal, India. The first step
involves the creation of classes and concepts which was focused o the student, lecturers and course.
Object properties were defined according to relationship which was added between classes. The
data properties of the university ontology were displayed which shows the relationship between
individual to data literal. Links were defined inside and between the classes created which showed
between Individual to individual. Other property is data property which show link between
individual to data type literal. Axioms were used to describe the relationship between classes,
attributes and individuals. Four axioms of classes were created: the existence of class, subclass,
equivalent class and disjoint with. All were described by language using rdf: id, rdfs: subClassOf,
owl: equiva-lentClass and owl: disjointwith. The axioms of attributes were used describe the
relations between attributes. In the ontology axioms was applied for providing a clear result of the
university term by search results, characteristics functional property was applied to object
property. Defining instances (individual) was done by first selecting the right class and then
creating its instances for the class, rdf: type was used to state its class. Reasoner was introduced to
check the consistency and also find the logic contradictions implicit in the definitions. The test of
knowledge consistency includes detecting its reflexive, transmission and redundancy of
knowledge.

Development, Deployment and Merging Aspects in Semantic web.

Based on Vishal et al research, one of the major functions of an ontology is to define set of classes
that together cover a domain of interest. Using protégé version 3.4.1, an ontology for an institute
department was developed. RDF were used to describe the identify the resources which were
available on the web and also describe the relationship between them. The project was deployed
using Jena framework and pellet reasoner which were then used for the creation of the object of
the ModelMaker class and creating the basic model by using the ModelMaker object. The protégé
PromptTab was used for the merging of ontologies which makes it possible to define common
concepts of two ontologies represented by a single ontology rather than using them separately.

Combining Ontology Development Methodologies and Semantic Web Platforms for

E-government Domain Ontology Development

Jean and Magda (2011), believes that semantic-based E-government involves describing
existing entities, concepts, processes, laws and regulations being used in governing a specific
government service domain, into a conceptual model domain ontology that is first represented in
a human readable form then transformed into a machine processable form using XML, RDF,
OWL. The research was conducted using Protégé and Java Jena ontology API. The Ushold and
King ontology building methodology was adopted for the building of the domain ontology
describing the semantic content pf the government service domain. UML was then used to semi-
formally represent the domain ontology. Then the Protégé and Jena API was then used to create
the Web Ontology Language (OWL) and Resource Description Framework (RDF) representations
of the domain ontology respectively to enable its computer processing. The ontology development
begins with specification phase which is where the aims and roles of the intended ontology and
the people who will be using it is specified. The next phase is the conceptualization phase this is
where a conceptual or domain ontology is built (representation, a conceptual or domain ontology
is a graph where the vertices are objects, concepts, and entities of the domain, and the edges are
lines interconnecting pairs of vertices and representing the relationships between the constituents
of the domain). The formalization phase involves the transformation of the conceptual and domain
ontology into its semi-formal representation using description logic and UML formalisms. The
semi-formal version of the ontology is then formally represented into a Semantic Web language
using protégé. The formal representation is then now deployed using web programming platform
(java, C++) that provides facilities for database storage and querying of the ontology developed.

An Agile Methodology for Ontology Development.

According to Abdelghany et al (2018), ontology engineering is a new field that focuses on
principles methods, methodologies and tools for creating and managing ontologies. The aim of
this field is the inclusion of explicit knowledge in software application, enterprises and business
procedures for a specific domain. He furthermore describes some method of developing ontologies
which are using the Cyc method, Uschold and King’s method, Grüninger and Fox’s methodology,
Methontology, KACTUS, SENSUS and On-To-Knowledge. The major challenges in ontology
development working with people, gathering requirements form a diverse set of users, prioritizing
these requirements, keeping domain experts engaged and responding to changing knowledge. And
also, to build ontologies that are dependable, stand the test of time and are ever evolving, they
should be supported by the software engineering methods and practices.
Abdelghany et al (2018), work proposes a way of adapting the agile principles and practices from
software engineering into the development of ontologies. This process revolves around three
phases: pre-game, development, and post-game. The pre-game phase involves the discovering of
the ontology goal and scope, tools and techniques, competency questions and available sources.
The development phase involves multiple and iterative cycles that are called sprints. Each sprint
involves: sprint planning, knowledge acquisition, conceptualization, formalization, integration and
sprint review. The post-game phase is the final phase which include: evaluation (verification and
validation), and maintenance.
The methodology was developed using the Software Project Time Management (SPTM), which
aimed at establishing a common understanding of the meaning of term used by the tools that
support this process. The SPTM ontology was also used as an intimidator to map concepts and
services used by these tools. The scope of the SPTM ontology focuses on the process as defined
in the PMBOK. The ontology requirements were formulated as competency questions which were
prioritized using the Planning Poker agile technique. The ontology of the SPTM was developed in
three sprints using the sprint planning, knowledge acquisition, conceptualization, formalization,
integration and sprint review. The second and third sprint were integrated with the ontology
produced in the first sprints. The FaCT++ reasoner and Protégé were used to ensure the SPTM
ontology consistency. The classes that were inconsistent were highlighted in red in a class called
nothing. A comparative assessment was carried out against existing methodologies with
compliance with IEEE standards. The result shows that using this approach reduces the complexity
of ontology development activities, improving communication between ontology engineers and
domain experts. It also showed that AMOD was easily followed during the ontology development.

Ontology development for unified traditional Chinese medical language system

Traditional Chinese medicine (TCM) as a complete knowledge system researches into

human health conditions via a different approach compared to orthodox medicine. A unified
traditional Chinese medical language system (UTCMLS) was developed using an ontology
approach that support TCM language, knowledge storage, concept-based information retrieval and
information integration. The TCM domain ontology was designed to conform with several
principles: refinement is needed, development is based on informal ontologies, evaluation is
essential and important, and the methodology of distributed loosely coupled is required. The
knowledge acquisition procedure adhered to some theory: deep analysis of specialized lexicons at
the knowledge center, a good construction of the TCM oriented concept framework and efficient
combination of controlled vocabularies and specialized lexicons. For the integration and merging
of the TCM ontology a top-down approach was used which involved the creation of 14 sub-
ontologies and six core top-level classes which was distributed to the domain expert of research
organizations in China. The bottom-up approach was used to the development of each of the sub-
ontology which made provision for information integration. IMPORT plug-in was then used to
merge the sub-ontologies from the different sources to unified TCM ontology.

Collaborative Ontology Development for the Semantic Web

York et al, describes Ontologies as an important role for these knowledge intensive applications
as a source of formally defined terms for communication. They aim at capturing domain
knowledge in a generic way and provide a commonly agreed understanding of a domain, which
may be reused, shared, and operationalized across applications and groups. However, because of
the size of ontologies, their complexity, their formal underpinnings and the necessity to come
towards a shared understanding within a group of people, ontologies are still far from being a
commodity. They designed an ontology-based portal for their institution (AIFB). The web
application was created for the presentation of information to humans and for software agents to
take advantage of its semantic structure. The intended target of the portal were the lecturers and
students and also to present typical information about persons, teaching-related topics and
research-related topics. The project was ontology was created to deal with: modeling navigational
structures, the research topics investigated by different groups of the institute, topics related to
teaching and personal information about members of the institute. In the requirement specification
phase, the requirements specification of the ontology was determined. To gather the initial
structures, a large set of research topics, topics related to teaching and personal information was
collected. In the refinement phase, the first draft of the ontology was refined by structuring the
concept hierarchy and addition of concepts, relationships and axioms. In the evaluation phase the
ontology is evaluated according to the previously set up requirement specifications. This phase
aims at refining the semi-formal description of the ontology according to the captured requirement
into a mature ontology, which is the output phase.

Customizable Workflow Support for Collaborative Ontology Development

Collaborative ontology development has become an active area of research and practice. On most
large projects today, ontology development is a collaborative effort, involving both ontology
engineers and domain experts. With larger groups of users contributing to ontology content, many
organizations define formal workflows for collaborative development, describing how project
participants reach consensus on definitions, who can perform changes, who can comment on them,
when ontology changes become public and so on. The architecture for supporting a customizable
workflow for collaboration ontology development was developed using protégé. The architecture
was developed in three major steps: the description level being the workflow ontology, it defines
what components a workflow can have. It lays out a formal language for describing workflows for
collaborative ontology development. The ontology contains the generic notion of roles, activities,
tasks, and control structures. The instantiation step is where user roles are specified, what activities
users with each role can perform, the order of activities, and the conditions that trigger new actions
or new workflows. Finally, in the ontology development, a workflow execution engine interacts
with the Protégé environment and controls the flow of operations in which the distributed clients
participate and generates a custom- tailored ontology-development environment that reflects the
workflows for the specific project. The workflow engine maintains the state of the workflow and
provides logging services to track all events and actions in the workflow execution.

Test-driven Ontology Development in Protégé

Test-driven development (TDD) is one of such methodologies in which the specification of

requirements for a software artifact and the subsequent verification of the specification is done by
means of test cases. The TDD process involves small iterations in which developers first specify
a number of test cases, then provide an implementation, and finally verify it by running the test
cases. Test-driven ontology development (TDD) is an ontology development process that involves
the specification of requirement with respect to the part of the target ontology. The TDD work-
flow starts with either an empty or an existing ontology that needs to the extended. The process
involves four major activities: the first step is the define phase, this is where the developer defines
the test cases. (positive and negative cases). For each of the cases an axiom is specified that entailed
in the case of positive cases (for the test to pass), and must not to be entailed in the case of negative
of a negative test case (for the test to pass). A positive test case can be seen as a check that the
ontology under test contains enough (correct) axioms such that the specified axiom holds as an
entailment. A negative test case can be seen as a check that the ontology under test does not contain
axioms such that the specified GCI holds as an entailment. In the testing phase the developer
executes the test cases and if all the test cases pass the TDD iteration is finished. As a result, the
ontology under test corresponds to the intended one with respect to the portions covered by the
test cases. In this case, the developer can return to the specification of further test cases or finish
the TTD process, meaning that no further test cases are envisaged. The implementation stage was
done using protégé. The added value of adhering to the suggested TDD paradigm is that it helps
the developer to differentiate between ontology parts that need further implementation (addition
of axioms) and those that require refactoring (deletion or modification of axioms), based on the
outcome of test case verifications. The final stage id the debug stage, this stage begins when the
test case has been executed and one or more of them failed. The goal of this procedure is to
determine the faulty axioms in the ontology and to support the developer while repairing those
axioms. Considering the complexity of inferences possible in expressive languages.

CONCLUSION

Ontology represents information in a manner so that this information can also be used by machines
not only for displaying, but also for automating, integrating, and reusing the same information
across various applications. In this paper, we have been able to review some system that has been
developed using protégé, we also highlighted the architecture, application areas, software used in
developing, user interfaces and ontologies.
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