Applied Computing and Informatics 14 (2018) 116–126

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Applied Computing and Informatics

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The use of ontologies for effective knowledge modelling and information

retrieval
Kamran Munir a,⇑, M. Sheraz Anjum b
a
Department of Computer Science and Creative Technologies, University of the West of England, BS16 1QY Bristol, United Kingdom
b
School of Electrical Engineering and Computer Science, National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan

a r t i c l e i n f o a b s t r a c t

Article history: The dramatic increase in the use of knowledge discovery applications requires end users to write complex
Received 21 February 2017 database search requests to retrieve information. Such users are not only expected to grasp the structural
Revised 30 July 2017 complexity of complex databases but also the semantic relationships between data stored in databases.
Accepted 31 July 2017
In order to overcome such difficulties, researchers have been focusing on knowledge representation and
Available online 7 August 2017
interactive query generation through ontologies, with particular emphasis on improving the interface
between data and search requests in order to bring the result sets closer to users research requirements.
Keywords:
This paper discusses ontology-based information retrieval approaches and techniques by taking into con-
Information systems
Ontology
sideration the aspects of ontology modelling, processing and the translation of ontological knowledge
Domain knowledge into database search requests. It also extensively compares the existing ontology-to-database transfor-
Database mation and mapping approaches in terms of loss of data and semantics, structural mapping and domain
Information retrieval knowledge applicability. The research outcomes, recommendations and future challenges presented in
Knowledge management this paper can bridge the gap between ontology and relational models to generate precise search requests
using ontologies. Moreover, the comparison presented between various ontology-based information
retrieval, database-to-ontology transformations and ontology-to-database mappings approaches pro-
vides a reference for enhancing the searching capabilities of massively loaded information management
systems.
Ó 2017 The Authors. Production and hosting by Elsevier B.V. on behalf of King Saud University. This is an
open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
2. Ontologies and knowledge representation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
3. Ontology-based information retrieval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
3.1. Information retrieval from a historical perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
3.2. Ontology-based query formulation approaches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
3.3. Ontology-based information linking approaches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
3.4. Ontology-based query refinement approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
4. Discussion: ontology-based information retrieval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5. Approaches to perform database-to-ontology transformations and to define ontology-to-database mappings . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5.1. Ontology-to-database mapping approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.2. Database-to-ontology transformation approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

⇑ Corresponding author.
E-mail address: [email protected] (K. Munir).
Peer review under responsibility of King Saud University.

Production and hosting by Elsevier

http://dx.doi.org/10.1016/j.aci.2017.07.003
2210-8327/Ó 2017 The Authors. Production and hosting by Elsevier B.V. on behalf of King Saud University.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126 117

5.3. Ontology-to-conceptual data model. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

6. Discussion: database-to-ontology transformation and mappings approaches for relational query formulation . . . . . . . . . . . . . . . . . . . . . . . . . . 123
7. Future opportunities and challenges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

1. Introduction in relation to ontology-based information retrieval. Section 5

reviews the state of the art database schema to ontology schema
In information management systems, structured query formu- transformation and ontology-to-database mapping approaches in
lation languages are one means of retrieving information. Writing terms of loss of data and semantics, structural mapping and
structured queries is a powerful method to access data since it domain knowledge applicability. Section 6 provides a discussion
allows end-users to formulate complex database queries by learn- and highlights a possibility of combining database-to-ontology
ing specialised query languages. However, query formulation with transformation and ontology-to-database mappings approaches
the exception of a few visual query generation and refinement for relational query formulation. Finally, Section 7 outlines the
approaches remains appreciatively difficult for the various levels future challenges and possible research directions towards using
of systems users. In recent years information retrieval has turned ontologies for information retrieval from information and Big data
out to be more complicated with the increased use of data mining, management systems.
decision support and business analytics applications. Conse-
quently, researchers focus has been on approaches that include
2. Ontologies and knowledge representation
visual database interfaces [1] and interactive query generation
through graphs [2,3], with a particular emphasis on providing
Over the past few years, many ontology development and query
interactive natural language interfaces to support query generation.
languages have been developed and this is still a continuing effort.
Recently, semantic-based approaches using domain ontologies have
While building an ontology-based system, it first requires deciding
been adapted for data modelling and information retrieval.
which ontology language is to be used in a given context. Numer-
Ontology-based information retrieval, for example as in [4–6] mainly
ous ontology languages were developed in the last few years. Most
aim at improving the interface between data and search requests
of these are based on the eXtensible Markup Language (XML) [9]
in order to bring the result sets closer to the users’ research
which enables them to be machine interpretable [10]. Notable
requirements. In general, an ontology represents a shared, agreed
examples are the Resource Description Framework (RDF) and
and detailed model (or set of concepts) of a certain problem
RDF Schema [11], the DARPA Agent Markup Language and the
domain [7]. One major advantage of using a domain ontology is
Ontology Inference Layer (DAML + OIL) [12], and the Ontology
its ability to define a semantic model of the data combined with
Web language (OWL) [13] and OWL2 [14]. In order to use ontolo-
the associated domain knowledge. Ontologies can also be used to
gies for query formulation it is important to evaluate them in terms
define links between different types of semantic knowledge. Thus,
of their expressive power, tools and reasoning support in order to
ontologies can be used in formulating some data searching
decide which ontology language is best suitable for this task. Most
strategies.
developments in the latest ontology languages are influenced by
This paper discusses ontology-based information retrieval
the RDF/RDFS XML based language rules and ranking structure.
approaches by taking into consideration the aspects of:
OWL has three sublanguages: OWL-Lite, OWL-DL and OWL-Full;
it was developed on top of RDF and DAML + OIL [15] providing
(a) ontology generation from database schema(s);
gradually more expressiveness power. The Semantic Web Rule
(b) processing of domain knowledge to represent it as ontological
Language (SWRL) [16] adds rules to OWL-DL (to increase its
knowledge; and
expressiveness) and is a combination of the OWL-DL and sublan-
(c) the translation of such ontological knowledge into relational
guages of the Rule Markup Language such as First Order Language.
database queries.
The basic idea of SWRL is to extend OWL-DL. It is simple and has
tight integration with the existing OWL language; this can be con-
Moreover, it provides a comparison between ontology-to-
sidered as a key characteristic of SWRL. Recently, OWL2 [14] has
database transformation and mapping approaches in terms of: loss
been developed on the existing structure to OWL (OWL1) i.e. all
of data and semantics;
the building blocks of OWL2 are present in OWL1; therefore all
OWL1 ontologies remain valid OWL2 ontologies [14]. There are
structural mapping; and
three new profiles of OWL 2: (1) OWL 2-EL, (2) OWL 2-QL, and
domain knowledge applicability.

Table 1
The outcomes presented in this paper can be beneficial in bridg-
Comparison between RDF(s), OWL-1 and OWL-2 showing possible uses of knowledge
ing the gap between ontology and relational models while representation concepts to formulate ontology based relational database queries.
attempting to generate precise search requests from ontology
Concepts RDF(s) OWL 1 OWL 2
expressions. Moreover, the comparison presented between various
ontology-based information retrieval, database-to-ontology trans- Formal semantics U U U
Equivalence  U U
formations and ontology-to-database mappings tools/approaches
Class definitions  U U
provides a reference for enhancing the searching capabilities of Constraints  U U
massively loaded information and management systems [8]. Enumerations  U U
After having introduced the motivation and context, the Cardinality constraints  U U
remainder of this paper is divided into the following sections. Inference  U U
Property chains   U
Section 2 introduces ontologies and domain knowledge represen- Disjoint properties   U
tations. Section 3 reviews the state of the art in ontology-based Qualified cardinality restrictions   U
database information retrieval. Section 4 discusses our findings
118 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126

(3) OWL 2-RL. These profiles are syntactic subsets of OWL 2 con- such systems have been reported in the literature (e.g., TAMBIS
structs. Selection between these profiles depends on the reasoning [20], GRQL [21], SEWASIE [22], Ontogator [23], OntoViews [24],
tasks and ontology structure. A comparison between RDF(s), OWL- OntoQF [25], VISAGE [26], Smartch [27], Semantic-based [28] and
1 and OWL-2 showing the possible uses of knowledge representa- many others). In most of these ontology based visual query formu-
tion concepts to formulate ontology based relational database lation systems, the search queries are performed using an ontology
queries is presented in Table 1. In summary, both OWL and RDF browser that visualises the ontology as a tree. The actual search is
have many common features, but OWL is a stronger language with done via concept selection through a visual tree or through key-
greater machine interpretability than RDF. Moreover, OWL comes words annotated by the visual ontology concepts.
with a larger vocabulary and a stronger syntax than RDF, which The TAMBIS system [20] supports the specialisation or general-
can be used to define complex ontology concept restrictions and isation of the base or filler ontology concepts to build database
subsequently to formulate ontology based relational database specific queries interactively. Here the data in the databases are
queries. stored (linked) as instances of ontology concepts. This approach
can be applied to resolve integration problems, where all informa-
tion sources have the same schema or provide nearly the same
3. Ontology-based information retrieval
view of a domain. Another similar approach based on ontological
graph pattern queries is presented in GRQL [21] and Knowl-
This section reviews the state of the art in ontology-based data-
edgeSifter [29]. GRQL relies on the full power of the RDF/S data
base information retrieval. Here, a historical overview of informa-
model and provides a GUI for building queries based on ontology
tion retrieval approaches is first presented, followed by a detailed
navigation. In this approach, queries are constructed by graphically
analysis of existing ontology-based query systems and data search
navigating through individual RDF/S classes and property
strategies in relation to three different key aspects that guided the
definitions. In SEWASIE (SEmantic Webs and AgentS in Integrated
review of such work. These three aspects are: (1) ontology assisted
Economies) [22], the principles of designing and developing an
visual or interactive query formulation; (2) ontology based infor-
ontology-based query interface are presented. The query interface
mation linking approaches (also known as keyword search); and
of SEWASIE supports the user in formulating a query through an
(3) ontology based query refinement (including query enrichment).
iterative refinement process supported by ontology navigation
where in the query formulation process, a user can specify a
3.1. Information retrieval from a historical perspective request using generic terms, can refine some terms of a query or
can introduce new terms, and can iterate the process if needed.
Database information retrieval is the search for information in In OntoQF [25] OWL-DL ontologies have been used for informa-
databases. The need for effective methods to automate information tion retrieval by automatically generating relational database
retrieval has grown in importance because of the significant queries using pre-stored domain knowledge. In comparison to
increase in the amount of both structured and unstructured infor- other existing approaches, one of the main features of OntoQF
mation embodied in information sources. Over the years, many approach is that it uses a combination of both database-to-
visual information retrieval approaches came into existence which ontology transformation and mappings to enable the automatic
aim to reduce the end users effort while interacting with data- query formulation process, which helps in generating precise data-
bases. These approaches intend to extract information from data- base queries. Overall, OntoQF uses a two-phase approach. In the
bases using visual tools. Such approaches include form-based first pre-processing phase, domain ontology is generated from rela-
[17], query by example (QBE) [18] or query by template (QBT) tional schema and related mappings are defined which links the
[19] etc. These approaches work for basic relational database domain ontology concepts to relational entities/columns and vice
queries, primarily because tabular structure of the database fits versa [30]. Moreover, the domain experts can specify studies as
well with the tabular skeletons used in query interfaces. However, ontology statements using a visual ontology query editor. OntoQF
such approaches do not help in semantic data retrieval nor do they rules for ontology-based relational query formulation suggest that
provide any query formulation support to generate complex for such query formulation the generated domain ontology does
queries. not require the definition of datatype ranges [31] or specific con-
To overcome the shortcomings identified above, further imple- straints that are expressed in the database schema. Moreover,
mentation improvements were advocated. One example is QUICK the domain knowledge is to be expressed in terms of OWL-DL
(Universal Interface with Conceptual Knowledge) [18] that focuses assertions as concept restrictions, which need to be consistent with
on automating query formulation by exploiting ER conceptual the respective domain ontology schema. In the second translation
schema design knowledge. Unfortunately, in the real world the phase, the OntoQF engine translates ontology statements into the
ER model has been used primarily for database design and they corresponding relational query statements. OntoQFs approach is
often do not store domain knowledge. Therefore, the ER based suitable for those systems or data mining applications that aim
query formulation approaches cannot provide a reliable method to keep all data at the original location(s) and use domain ontology
to depend on its comprehensiveness in expressing low-level query for knowledge-based information retrieval [25].
constraints. More recently, several ontology languages with prop- The system presented in [32] provides interactive database
erly specified semantics have been developed. Several ontology- query generation through non-directed graphs supporting natural
based approaches have been reported in the literature that can languages. The ontology language used in this system is based on
provide intelligent query formulation services for relational data- the RDF structure. In order to construct queries, query terms are
bases. Such approaches are reviewed in the following sections. suggested to a user in a natural language from a predefined vocab-
ulary. In a report of the EU Translational Research and Patient
3.2. Ontology-based query formulation approaches Safety in Europe (TRANSFoRm) [33], a query and data extraction
workbench has been presented. The TRANSFoRm query formula-
Ontology-based Visual or Interactive query formulation systems tion workbench software tool provides interfaces to author, store
are query systems for databases that use visual representations to and deploy queries of clinical data in order to identify subjects
express related data requests. These systems adapt ontologies for for clinical studies. Moreover, TRANSFoRm query formulation
database query generation in order to improve the effectiveness workbench enables users to define criteria groups flexibly, whilst
of the human-computer communication. In recent years, many catering for complex queries with combinations of operators.
 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126 119

Table 2
Comparison of ontology-based query formulation tools/approaches.

Tools/approaches Query support by Query support Replication of data not Supports Heterogeneous data- Natural
semantic clause by text required in ontology multimedia sources support language query
database
CROEQS [34] U U U U
GRQL [21] U U
Ontogator [23] U U U
OntoQF [25] U U U
OntoViews [24] U U U
Smartch [27] U U
SEWASIE [22] U U U U
TAMBIS [4,20] U U
TRANSFoRm [33] U U U U
VISAGE [26] U U U U
Ontology and Natural Language [35] U U U
OPTIQUE [36] U U U
KIRA [37] U U U U U
ATHENA [38] U U U
Using ontology SPARQL [39] U
Pay-As-You-Go Method [40] U U
Ontop [41,42] U U U
Querying via OWL 2 QL [43] U U

The search method of ontology-based image retrieval systems [44]. Another ontology-based information linking approach with
such as Ontogator [23], and OntoViews [24] are examples of a similar techniques, but for query refinement purposes, is presented
concept-based multi-facet search using RDFS ontologies. In a in [45,46]. This approach stores concepts from a data source as part
multi-facet search, multiple distinct views are augmented to data of the ontology and links actual data with ontology concepts. The
created via ontology projection [24]. OntoViews, supports seman- query answers are improved by using the semantic knowledge
tic auto-completion of a query [24]. It uses a keyword search expressed in an ontology. Database queries are transformed by
mechanism for ontology navigation. The search keywords are using is-a, part-of and sync-of relationships between ontology
linked directly to ontology classes. A user search request is pro- concepts.
cessed as a multi-facet search and results are delivered in a web The work carried out in designing ontology-based interactive
browser. Once a single interesting instance (at least) has been information retrieval interfaces [47] provides an ontology-based
found, additional information can be retrieved via ontology web information retrieval system. This approach works as an inter-
browsing. active information retrieval system where end-users are guided
Effective information retrieval is becoming more challenging through an ontology (OWL-based) driven graphical interface to
with the increase in the use of Multimedia databases, which are define the search criteria. This work mainly addresses the problem
usually bigger than traditional databases. In [34] a semantic search of ‘‘where to start in the usage of an ontology-based IR interface”;
engine for multimedia databases namely CROEQS is presented that that is, which elements of the ontology should be provided to the
works as both ontology-based query translator and text based user to begin the search specification [47]. Accordingly, a user first
search engine. In relation to the use of ontologies for the provision selects a relevant domain in order to start building a query. The
of intelligent and accurate search engines Kunmei Wen [27] pro- interface then provides a number of search entry points along with
posed Smartch, which is an ontology-based search engine. In this their descriptions. Once the user selects the desired ontology ele-
approach, a ranking method is proposed while searching for con- ments, web information elements are retrieved by following the
cepts, instances and the relationships between them. In Smartch, static ontology-to-web links.
the end-users’ search is performed by keywords. Once results are In the SemanticLIFE project [48], a front-end approach guides
retrieved end users’ can use the graphical user interface of Smartch the users in generating data requests. The SemanticLIFE system
to view all instances of an ontology concept, view relationship integrates multiple data sources and stores them in an ontological
between two entities and view all instances of a user defined con- repository. The Virtual Query component of the SemanticLIFE sys-
cept. Table 2 presents a comparison between some of the major tem allows semantic query writing on the ontological RDF-based
ontology-based query formulation tools and approaches. repository. Users are provided with an overview about the system
data through a Virtual Data component which stores the extracted
metadata of the data sources in the form of an ontology. The
3.3. Ontology-based information linking approaches approach provides a query engine, which recommends the query
patterns according to the users’ querying context. Since it is based
The work carried out in the European TONES project [44] pro- on a common ontology mapped from the local data source ontolo-
vides relational database access through ontologies. In this gies, this approach can refine users’ queries and create sub-queries
approach, data access is enabled by defining links between ontol- over the local data sources.
ogy concepts and relational data. This ontology-to-database map-
ping mechanism enables a designer to link a data source to an
OWL-Lite ontology. While defining mappings, the designer needs 3.4. Ontology-based query refinement approaches
to take into account that an ad-hoc identifier should denote each
concept instance so that instance values cannot be confused with Ontology-based query refinement approaches aim at enabling
data items in the data source. Queries are formulated by consulting end-users to make an improved formulated query. These
ontology-to-database mapping rules, but this rule derivation pro- approaches attempt to improve information retrieval by replacing
cess is carried out manually by ontology and database experts or adding extra terms into an initial query. Most of the existing
120 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126

query refinement approaches include both query rewriting and [44,46,58,48] etc.) store all data from a data-source as part of the
expansion operations. Using these approaches end-users are pro- ontology (as ontology instances) or link it directly to ontology con-
vided interaction with candidate expansion terms based on con- cepts. But, often it is not practically feasible to store all data as part
cept hierarchies which stem naturally from the developed of a certain domain ontology, especially for systems with large
domain ontologies and associated ontological schema. This section amounts of data. Data that are stored as part of the ontology often
discusses these ontology-based query refinement techniques that need to be loaded in memory to perform the Select query opera-
have been introduced over the past few years such as Thesaurus tions. Moreover, this may become both a complex and time con-
Ontology Navigation [49,50], Ambiguity-Driven [51,52], suming activity to directly link all database instances to
Information-Need Driven [53] etc. associated ontological concepts. Furthermore, it appears that a lim-
Query expansion implementations (e.g. [49,50]) use thesaurus ited number of query formulation approaches reviewed in the lit-
ontology navigation for query expansion. These approaches use erature review build on the assertion capabilities of ontologies.
the WordNet ontology (http://wordnet.priceton.edu) for query Thus, it can clearly be deduced that these approaches need to be
expansion and adapt basic keyword search mechanisms using key- extended to include further details, such as what needs to be
words, which are identified in the ontology for a matching concept. included in the ontology from database along with the domain
Another approach based on this thesaurus ontology navigation knowledge needed to initiate the query formulation process, to
approach is the Knowledge Sifter [29]. Knowledge Sifter is a scale- enable ontology-based query formulation based on the ontology
able agent-based system that supports access to heterogeneous semantic and assertion capabilities.
information sources and relies on the agents technology for query As discussed before, a domain ontology could be used for repre-
refinement. In this approach, a user query formulation agent sup- senting domain metadata with related semantics extracted from
ports user query specification to access multiple ontologies using the relational database schema. To achieve this, first there is the
an integrated conceptual model expressed in the OWL. This user need:
query formulation agent also consults the ontology agent to refine
or to generalise a query based on the semantics provided by the 1. to identify the extent to which domain metadata and relation-
ontology. ships from a relational database can be transformed into a
In QuOnto [54] and MASTRO [55], the query answering process domain ontology schema, and
is performed through query rewriting. Both of the MASTRO and 2. to identify a systemic approach to transform this selected
QuOnto systems adapt a similar ontology based query answering domain metadata and relationships into the domain ontology
service [55]. In these approaches, end-user queries are first refor- schema.
mulated on the basis of ontological intensional knowledge, and
then they are evaluated by a database engine using a means of Moreover, a description logic based knowledge representation
predefined mappings. Database views are defined for ontology formalism is well suited for modelling domain knowledge (also
concepts and roles using SQL queries are specified in ontology- called assertional knowledge) in a domain ontology in terms of
to-database mapping declarations. In [56] an ontology-based tool concepts and properties. However it may not be necessary or even
to convert a natural language query into nRQL query has been pro- possible to use all of OWLs description logic constructs for formu-
posed. To achieve the conversion, first a pre-populated dictionary lating queries. Therefore, there is a need to identify OWL constructs
is used to search the synonyms of query terms. If no matching that can be utilised to specify domain specific knowledge as con-
records are found then the ontology search is performed, which cept restrictions for the purpose of formulating relational database
results in extracting a sequence of entities represented in form of queries. In addition, there are significant differences between OWL
triples. Finally, nRQL query is generated based on the resultant ontology statement constructs and relational query statement con-
information. The ontology-based query refinement approaches structs. Furthermore, the OWL concept restrictions could be either
such as the Step-By-Step Query Refinement [52], examine query simple or complex potentially involving many conditions. As a con-
ambiguity in relation to both structural and semantic ambiguities. sequence, ontology-driven relational query formulation is not only
Structural ambiguity deals with the actual structure of a query that dependent on the underlying relational database schema structure,
is analysed with respect to the underlying ontological knowledge. but also on the translation of individual and different combinations
In the case where a conflict is detected, alternative suggestions are of ontology statement constructs into relational query statement
retrieved and presented to the end-user for selection. constructs.
An ontology guided (relational) query formulation process also
needs to take into consideration aspects of ontology modelling,
4. Discussion: ontology-based information retrieval processing and integration of domain knowledge based on the
underlying relational database models and mapping to ontological
In Section 2, benefits, weaknesses, power and effectiveness of queries to a relational database schema. The following sections
current mature ontology development languages in relation to first review the state of the art in this field and build a case to
query formulation have been highlighted, and it has been noted inform the usability of combining both ontology-to-database
that OWL has greater support for expressing semantics when com- transformation and mapping approaches for relational database
pared to RDF and RDFS. According to the literature review of query formulation.
ontology-based information retrieval in Section 3, it appeared that
the focus has been on (1) visual or interactive query formulation;
(2) information linking approaches; and (3) query refinement 5. Approaches to perform database-to-ontology
approaches. Ontology based visual or interactive database query transformations and to define ontology-to-database mappings
formulation systems use visual representations to express the
search criteria. Most of these systems are based on the RDF struc- In order to specify the schema structure of a domain ontology
ture and support the specialisation or generalisation of the base or for relational query formulation, one requirement is to represent
filler ontology concepts in order to build database specific queries the domain metadata along with the semantic relationships in
interactively. However, it may be concluded that much of this work the underlying relational database schema into the ontology
has been (e.g., [57,21,29] etc.) towards interactive query genera- schema. Thus, to represent a relational data model in an ontology
tion through nondirected graphs. Other approaches (e.g., model, the transformation of the relational model into the ontol-
 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126 121

ogy model remains an essential requirement in order to achieve mapping situations arising from low similarity between ontology
correct transformations. This is because an ontology generally con- and database models [62]. The mapping definitions generated by
tains the definition of the concepts and their relationships for a R2O are not intended to be generated manually, and therefore they
given domain, as well as the domain rules (e.g. cardinality, disjoint- cannot be read or updated without using its specific GUI. Such an
ness etc.) that restrict the semantics of concepts and the concep- ontology-to-database mapping approach is not sufficient to be
tual relationships in a specific conceptualisation of a particular used for ontology creation for query formulation.
application domain. In contrast a relational data model, on the con- An approach for automatic database to ontology mapping that
trary, represents the structure and semantic data integrity of a satisfies both information and query preservations properties of
given database application [59]. To provide detail this section semantic mapping is presented in [74]. Here, information preser-
reviews the existing database-to-ontology transformation and vation is the ability to recreate original database from mapping
mapping approaches. These approaches are reviewed in terms of results and query preservation is the ability to translate each rela-
the loss of data and semantics, structural mapping, domain appli- tional query over a relational database into an equivalent semantic
cability and correctness. query over resulting RDF graph. D2RQ [69] extracts the contents of
Currently, there are several tools and approaches available that a relational database to an RDF graph as per the mappings specified
can be used to define mappings between ontology schema and in a mapping language which is also expressed in RDF. Another tool
database schema (called ontology-to-database mappings) such as that is heavily influenced by D2RQ [69] is Automapper [75].
D2R-MAP [60], extended D2R [61], R2O [62], VisAVis [63], in [64] Automapper creates an OWL ontology through SPARQL [76] to
and many others. These approaches are based on the assumption describe a relational schema. The feature that separates Automap-
that both the database and the ontology pre-exist, and produce a per from other ontology mapping approaches is that the generated
set of corresponding mappings between the relational database OWL ontology is also enhanced with SWRL [16] rules to express
schema and the ontology schema. These mapping approaches are the constraints, such as the primary key or attribute datatype
different from the transformation approaches, which aim at gener- restrictions.
ating an ontology model from a relational model (called database- In [77] a three phased approach to extract ontology from a rela-
to-ontology transformations) as described in [65–67]. A majority of tional database is presented. In the first phase, ontology TBox is
these approaches provide trivial transformations, where each data- written using relational schema by generating classes from both
base table maps to an ontology class, each column to a datatype referenced and referencing columns. Here, the referencing column
property, each row to an instance and foreign key columns are used is defined as a subclass of the one related to the referenced column.
to link an instance of a class to instances of another class. In addition In the second phase, ABox is written using DB values, and in the
to these approaches, several database-to-ontology transformation final phase, reasoning is performed to extend the ontology.
tools have been developed. For example, DataGenie [68] is a In [78] an automated ontology construction approach is pre-
plug-in for Protégé [68] that imports data from a relational data- sented that considers relational schema. In addition to trivial table
base to an ontology, D2RQ [69] treats Non-RDF relational data- to class transformations, the proposed mappings in this approach
bases as virtual RDF graphs, D2RMAP [70] is a database to RDF include some additional rules in relation to a table key column(s)
mapping language and processor, RDB2Onto [71] works by creat- and other constraints. These include map foreign key column to
ing the semantic metadata from a relational database, RDB2ONT ontology object property and non-foreign key column to ontology
describes a formal algorithm to use the relational database meta- datatype property. Moreover, it maps primary key and unique con-
data plus structural constraints to construct an OWL ontology, straint to ontology InverseFunctionalProperty, and NULL constraint
and in [72] an approach to develop ontologies from relational data- to minCardinality constraint with minCardinalty of 1 [78]. Thus, this
bases using reverse engineering is presented. The following sec- approach can be useful for the transformation of both relational
tions discuss these approaches in more detail. database structure and its constraints to ontology. Table 3 presents
a comparison between some of the major database to ontology
5.1. Ontology-to-database mapping approaches mapping tools and approaches discussed in this section.

The ontology-to-database mapping approaches assume the 5.2. Database-to-ontology transformation approaches
existence of both a relational database and an ontology and pro-
duce a set of corresponding mappings between them [73]. The The database-to-ontology transformation approaches assume
related approaches are D2R-MAP [60], extended D2R [61], R2O that only a relational database exists while an ontology is produced
[62], VisAVis [63] and in [64]. These mapping approaches relate from the relational database by applying certain transformation
each construct in the relational database schema to a construct rules [73]. Such approaches include learning ontologies from rela-
in the ontology schema and ignore unrelated constructs between tional databases [65], mappings from relational to OWL model
them. The R2O (Relational to Ontology) [62] approach, for example, [66], relational databases to OWL ontology [67] and rule-based
is an extensible and declarative language to describe mappings transformation of SQL relational databases to OWL ontologies
between relational database schemas and ontologies implemented [84]. Most of these approaches result in specifying an ontology that
in RDF(S) or OWL. The most important aspect of this approach is has the same flat structure (i.e. classes and instances) as the original
the use of the database schema and the ontology without adapta- relational database (i.e. relations and columns). These approaches
tion. Also, this approach defines a declarative specification of the utilise automatic or semi-automatic transformations of relational
mappings between its modelling components. The ontology-to- databases to ontologies. Here the transformation is based on a
database mappings are defined as a set of mapping elements that set of rules specifying how to transform the constructs of a rela-
relate a relational DB schema to an ontology schema. This means tional model to develop an ontology with the relational model as
that database tables, columns, primary and foreign keys, etc., are its domain. The basic transformations adopted in these approaches
related to domain ontology concepts, attributes, relationships, etc. are very similar, where the constructs of a relational model such as
R2O is an extension of recent approaches such as D2R-MAP [60] tables, columns, datatypes and constraints are transformed in an
and extended D2R [61], which lack expressiveness in terms of writ- ontology model as classes, instances, properties and constraints,
ing complex mapping statements and are not considered fully respectfully. In such a scheme, a table is represented as a class
declarative [62]. As a consequence, the R2O mapping language unless all its columns are foreign keys to other tables. The reference
has been considered sufficiently expressive to cope with complex column of a foreign key is represented as an object property. A col-
122 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126

Table 3
Comparison of database to ontology mapping tools/techniques.

DB to ontology mapping tools/approaches Ontology to DB Mappings defined Mappings defined Maps DB instances
mapping support using ontology using XML to ontology
D2R-MAP [60] U U U
R2O [62] U U U
VisAVis [63] U U
OntoQF [30] U U U
Extended D2R [70] U U U
D2OMapper [68] U U U
Mapping DB to RDF and OWL [74] U U U
RDB2OWL [79] U U
BOOTOX [80] U U
RDF Graph from using SPARQL [81] U U U
RBA [82] U U
R2 BA [83] U U

umn is represented as a datatype property accompanied by a max- In OntoQF [25] an ontology is generated from a relational data-
imum cardinality of one, unless it is a foreign key. The column con- base (model) that stores the domain metadata, semantics and
straint Unique is represented as an inverse functional property. related domain knowledge. The major differences of this approach
Similarly, Not Null is represented as a minimum cardinality of with other approaches is that in OntoQF (1) the transactional data
one. A primary key is represented as both an inverse functional remains at the original data source(s); (2) in can handle the data-
property and a minimum cardinality of one. Finally, a row is repre- base relations up to third normal form; and (3) the resultant trans-
sented as an ontology instance. formation describes the original database relationships [25].
Another database-to-ontology transformation tool, RDB2ONT Moreover, in OntoQF, the ontological descriptions are based on
[85] can be used for generating OWL ontologies from relational domain metadata objects; and consequently, it supports changes
database systems. RDB2ONT describes a formal algorithm that uses and extensions to the underlying database schema. In [89], mod-
relational database metadata and structural constraints to con- elling of health service knowledge is done in terms of health ser-
struct an OWL ontology whilst preserving the structural con- vice ontology, where the health service ontology is defined from
straints of the underlying database [85]. The RDB2ONT tool has the perspective of concept hierarchy and ontology concepts. More-
two major components: the OWL Builder and the OWL Writer. over, the matchmaking algorithm in this approach is powered by
The OWL Builder extracts metadata and structural constraints from UMLS ontology. In [90] graph-based knowledge representation
a relational database system and builds a model. This model is then model has been used in query answering; in particular, a concep-
used to generate an OWL ontology describing the underlying data- tual graph model is used instead of knowledge representation for-
base. This approach is less complex when compared to D2R-MAP malisms as used in [25].
[60], D2R [69] or R2O [22] which are based on creating a new com- Table 4 presents a feature comparison between some of the
plicated mapping language. This is mainly due to its simplicity and major database to ontology transformation tools and approaches
easy of configuration for defining concrete data mappings. discussed in this section.
Triplify [86] is an RDF extraction tool from relational schemas,
which uses SQL queries to select subsets of the database schema 5.3. Ontology-to-conceptual data model
and maps them to ontology classes and properties. The advantages
of the Triplify tool include predefined configurations for the sche- Ontologies allow an interaction between data held in different
mas and the use of easily understandable SQL queries for the map- formats and can potentially be used as the basis to guide and val-
ping representation. Another such tool is SquirrelRDF [87], which idate models of particular domains. For example, a considerable
uses predefined mappings to extract database contents as RDF tri- amount of work has been reported which aims to transform
ples. Its use is fairly simple, but it does not offer the wide range of ontologies to conceptual data models (expressed, for example, in
features when compared to D2RQ [69] as explained earlier. Later, UML or in ER) in [98,99,72]. This section reviews the key relevant
Tether [88] has provided some refinements and solved several and mature ontology-to-database mapping approaches.
shortcomings of the native translation of a relational database to According to El-Ghalayini et. al. [98], a domain ontology can be
RDF approach. Most of these refinements; such as to reduce the mapped to a domain conceptual data model (CDM). In this
size of the RDF graph, were specific to cultural heritage domain. research, several mapping rules have been proposed that guide

Table 4
Comparison of database to ontology transformation tools/techniques.

Database to ontology transformation tools and/or approaches DB to ontology Output ontology Ontology extension Preserve structural
transformation support in OWL format by reasoning constraints
RDB2Onto [71] U U
RDB2ONT [85] U U U
Learning ontology from relational schema [78] U U U
Generating OWL ontology from RDB [77] U U U U
Learning ontology from RDB [65] U U U U
DB2OWL [91] U U U
OntoQF [25] U U U U
Mapping RDB to OWL structure [92] U U U
Transforming of RDB to OWL [93] U U U
RDB2RDF [94] U U
Mapping RDB into Ontology [95,96] U U U
A systematic mapping via reverse engineering [97] U U U
 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126 123

the transformation from a given domain ontology to a correspond- generated by applying database-to-ontology transformation rules.
ing conceptual schema. Another approach to building ontologies According to the database-to-ontology transformation approaches
from relational databases using reverse engineering is presented as discussed in this paper, the process of ontology construction
in [72]. Unlike RDB2ONT [85] and RDB2Onto [71], this approach from relational databases involves analysing the database schemas
does not directly transform a relational database into an ontology; to determine the database-to-ontology transformation dependen-
rather it uses an entity relationship model to reverse engineer a cies. This analysis helps in determining the relational entities that
domain ontology. In this approach, OWL-DL is used as an ontology may be transformed into ontology concepts. It also helps to group
representation language and ER for data modelling. The graph together or separate in occasions the information specified in a
transformation language, as in [100], is used for node and edge relational database table and to determine relationships between
addition into an ER model. The node addition operation is used to different tables. However, the database-to-ontology transforma-
introduce new objects into the ER model and the edge addition tion rules are solely dependent on application requirements. Most
operation to build relationships between ER objects. of the existing database-to-ontology transformation approaches do
Recently, an approach to transform a domain ontology into a not provide an exact representation of the domain-metadata in an
relational database has been presented [99] based on an algorithm ontology and also do not enable the generation of the respective
embedded in the OWL2DB [101]. In this approach, OWL documents database relations. Therefore, such transformation approaches do
are parsed in order to generate the corresponding Data Definition not particularly aid in the process of specifying concept restric-
Language (DDL) scripts. During the parsing and data transforma- tions, and also when generating complex database queries. In order
tion process, the system first transforms ontology classes into data- to overcome these shortcomings and to use ontology definitions
base table definitions; the next steps are transformations of object, for database information retrieval, a combination of both
datatype properties and constraints into complete DDL statements, database-to-ontology transformation and ontology-to-database
and finally, the database is filled with class instances. In order to mappings [25] may be utilised, which could be an interesting
transform ontology classes into relational database tables, the future challenge for the research community. More areas of future
approach uses a breadth-first search on the hierarchical levels of research are outlined in the following section.
the ontology classes [101]. As a result, one table in a relational
database is created for each class in an ontology with a one-to-
one relationship between classes and their subclasses. The OWL 7. Future opportunities and challenges
object properties are transformed into table relationships, which
again uses breadth-first search. Depending upon the local cardinal- Most of the existing approaches are based on using single
ity of class properties, one-to-many or many-to-many relationships domain ontology for generating relational database queries. Using
between tables are created. This approach can transform all OWL- such approach, database domain metadata and semantics can be
Lite syntax but only part of OWL-DL syntax. transformed into a domain ontology schema with domain knowl-
edge added as concept restrictions. It is possible to adapt the same
approach for multiple databases that are geographically dis-
6. Discussion: database-to-ontology transformation and tributed, but conceptually related with respect to a common sub-
mappings approaches for relational query formulation ject area; for example, a database that manages patients treatment
records and another that manages patients family history, where the
An ontology generally contains the definition of the concepts domain-subject is Patients. In such cases, an integrated ontology
and their relationships for a given domain, as well as the assertions needs to be developed to capture the common as well as the differ-
and domain rules (e.g. cardinality, disjointness etc.) that restrict the ent domain metadata and related semantics of the underlying dis-
semantics of concepts and the conceptual relationships in a speci- tributed databases. Moreover, the existing query formulation
fic conceptualisation of a particular application domain. A rela- frameworks should be extended to develop an approach to inte-
tional data model, on the contrary, represents the structure and grate related domain knowledge in order to obtain a unified
integrity of the data elements of the, in principle, single specific domain ontology that captures all of the domain concepts.
enterprise application(s) by which it is being used. A relational Moreover, in the past the focus has been on visual or interactive
database is a collection of relations (tables) and a relation consists query formulation, information linking and query refinement
of a relational schema and a relation instance. The relation schema approaches. Most of these ontology based visual or interactive
in a database consists of the schemas for the relations, whereas the database query formulation systems either use visual representa-
relation instances are sets of tuples, also called records. Moreover, tions to express the search criteria or they are based on the ontol-
each tuple is a row and all rows have the same number of fields ogy structure and support the specialisation or generalisation of
(columns). After reviewing such differences and similarities ontology concepts in order to build database specific queries inter-
between ontological and relational data models it has been noted actively. Other approaches store all data from a data-source as part
that ontologies are semantically richer than database (conceptual) of the ontology or link it to ontology concepts. However, it
schemas, because conceptual data models only aim at establishing appeared that, with the exception of few approaches, there is still
a link between users and domain requirements, and describe a log- a lack of knowledge-driven query formulation approaches that
ical structure of the data. An ontology can also be used to specify build on the assertion capabilities of OWL-DL such as OWL-2.
domain knowledge of a specific domain of interest. Moreover, Moreover, there is a need to extend the existence approaches to
ontologies can play a significant role in information system devel- answer the questions like: What needs to be included in the ontology
opment and have the ability to represent conceptual data models from database along with the domain knowledge needed to initiate the
using ontological theories, for example as reported by [98,30]. query formulation process, to enable ontology-based query formula-
Therefore, existing relational data models can be used to create tion based on the OWL-DL semantic and assertion capabilities. Plus
ontologies, while existing ontologies can be used to generate rela- how such domain knowledge can be automatically evolved and
tional (conceptual) schemas. extended within the existing domain ontology? Furthermore, this
Ontology-to-database mapping approaches assume the exis- work may be extended to further domains; and in particular, for
tence of both a relational database and a domain ontology. How- enhancing the searching capabilities of massively loaded informa-
ever, the database-to-ontology transformation approaches tion management systems such as national statistical survey portals
assume that only a relational database exists and an ontology is and context-aware environments that mobile devices are part of.
124 K. Munir, M. Sheraz Anjum / Applied Computing and Informatics 14 (2018) 116–126

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Dr. Kamran Munir has BSc, M.Sc. and Ph.D. in Computer Science from United
domain ontologies to conceptual data models, in: Proceedings of the 23rd
Kingdom. His primary research interests include Information Science, Big data,
IASTED International Conference on Databases and Applications, 2005, pp.
cloud computing, distributed data processing and knowledge management. He has
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[99] E. Vysniauskas, L. Nemuraite, Transforming ontology representation from contributed to the various European Commission projects: Asia Link STAFF (2004–
OWL to relational database, Inform. Technol. Control 35 (3A) (2006). 2006), Health-e-Child (2006–2010), neuGRID (2011–2014) and neuGRID4You
[100] P. Mitra, G. Wiederhold, M. Kersten, A graph oriented model for articulation (2013–2016) in which he led the Joint Research Area. His role also includes the
of ontology interdependencies, in: Proc. Extending Database Technologies, production and leadership of UK and international postgraduate computer science
Berlin Heidelberg, 2000, pp. 86–100. degree courses such as Big Data and Cloud Computing, and frequent collaborations
[101] A. Gali, C. Chen, K. Claypool, R. Uceda-Sosa, From ontology to relational with students and graduates, including the conduct of collaborative work and
databases, Conceptual Model. Adv. Appl. Domains 3289 (2005) 278–289. supervision of MPhil and PhD theses.
[102] M. Bilal, L.O. Oyedele, J. Qadir, K. Munir, S.O. Ajayi, O.O. Akinade, H.A.
Owolabi, H.A. Alaka, M. Pasha, Big data in the construction industry: a review M. Sheraz Anjum has obtained MS degree from National University of Sciences and
of present status, opportunities, and future trends, Adv. Eng. Inform. 30 (3) Technology (NUST) and currently doing PhD in Computer Science. His research
(2016) 500–521, http://dx.doi.org/10.1016/j.aei.2016.07.001. interests are in the areas of knowledge management, relational databases and Big
[103] M. Bilal, L.O. Oyedele, J. Qadir, K. Munir, O.O. Akinade, S.O. Ajayi, H.A. Alaka, H.
data.
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towards a plug-in for construction waste minimization using big data, Int. J.