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%   TITLE:          DBFOschemafy_V_3_001.tex
%   VERSION:        3-001
%   FACILITY:       entry point of the paper DBFOschemafy
%
%                   DBFOschemafy is an advanced Java-based ontology 
%                   engineering tool that leverages a relational database 
%                   for input, overcoming the scalability limitations of 
%                   its predecessor, OWLschemafy, which relied on text 
%                   files..
%
%   AUTHOR(S):      Hlaszny, Edit PhD [HED] edithlaszny@gmail.com
%   SUPERVISED BY:  -
%   CREATION DATE:  02-JAN-2025
%
%   ENVIRONMENT:    TeXstudio 4.8.1 
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%       04-JAN-2025 [HED]        3-001 first draw 
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%   name of the tool
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\newcommand{\DBFO} {D{\color{red}BFO}schemafy }
\newcommand{\DBFOcomma} {D{\color{red}BFO}schemafy, }

\pagestyle{fancy}
\fancyhead[L]{\scriptsize{\DBFO -- A DB-Driven, BFO
annotated Ontology Generator for Streamlined OWL}}
\fancyfoot[L]{\textcolor[RGB]{160,160,160}{\scriptsize{\raise0.3ex\hbox{\tiny{\textcopyright}} Edit Hlaszny, PhD | 02 Januar 2025}}}
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\title
{
    \fontsize{10pt}{12pt}\selectfont\sffamily
    \hspace{-20pt}
    \textbf{\DBFO -- A DB-Driven, BFO annotated
    Ontology Generator for Streamlined OWL}
    \par
    \vspace{12pt}
}

\author % and Abstract
{
    \fontsize{10pt}{10pt}\selectfont\sffamily
    \hspace{-18pt}
    Edit Hlaszny, PhD\\
    Dr Hlaszny Bioystems Engineering\\
    Mail: edit@edithlaszny.eu\\
    \hypersetup{hidelinks}\url{http://www.edithlaszny.eu/}\\
    Phone: +36 30 3116516
    \fontsize{10pt}{10pt}\selectfont\sffamily
    \\ \\ \textbf{Abstract}
    \vspace{4pt}\\
    \fontsize{8pt}{8pt}\selectfont\sffamily
       \DBFO is an advanced Java-based ontology engineering 
       tool that leverages a relational database for input, 
       overcoming the scalability limitations of its predecessor, 
       OWLschemafy
       (\fontsize{7pt}{7pt}{\textcolor[RGB]{0,0,255}{\hypersetup{hidelinks}\url{http://www.edithlaszny.eu/ontology/OWLschemafy/}}}),
       which relied on text files. This approach enables efficient management and manipulation of large-scale ontologies. \DBFO generates OWL ontologies with comprehensive annotations: Class entities are annotated in English, German,
       and Dutch, and full BFO 1.0\raise0.8ex\hbox{\tiny{ [1]}} annotations
       provide a robust and standardized framework for understanding the ontological 
       relationships between entities.
    \vspace{8pt}\\
    \fontsize{10pt}{10pt}\selectfont\sffamily
    \textbf{Keywords}
    \vspace{4pt}\\
    \fontsize{8pt}{8pt}\selectfont\sffamily
        Ontology Development, OWL-Generator, BFO Annotation, 
        Relational Database, Java Application.
}

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\section
{Introduction} 

    \subsection
    {The Significance of Ontologies in the Digital Age} % 1.1

    In today's data-rich world, the ability to effectively organize 
    and represent knowledge is crucial. Ontologies, with their formal
    and structured representation of concepts and their relationships,
    play a pivotal role in enabling knowledge sharing, interoperability,
    and intelligent data analysis.

    \vspace{4pt}
    This chapter introduces \DBFOcomma an innovative ontology engineering 
    tool that leverages a relational database (RDB) to streamline the
    creation of OWL\raise0.7ex\hbox{\tiny{
    [3]}}\raise0.7ex\hbox{\tiny{[4]}}\raise0.7ex\hbox{\tiny{[5]}} 
    ontologies.
    
    \showFig{./pictures/Fig_Overview.png}  % filename to be displayed
            {0.7}                   % width
            {\DBFO is an innovative software tool designed \\
             to streamline the process of ontology
             development\raise0.7ex\hbox{\tiny{
             [6]}}\raise0.7ex\hbox{\tiny{[7]}}.} {\raggedright}          % indentation
            {10pt}                   % space before
            {22pt}                  % horizontal shifting
            {-6pt}                  % space between figure and title
            {-8pt}                  % space after

    \DBFO is an innovative software tool designed to streamline the 
    process of ontology development. It leverages a relational 
    database (RDB) for efficient data management and manipulation, 
    overcoming the limitations of traditional text-based approaches. 
    This database-driven approach allows for the creation, management, 
    and refinement of large-scale ontologies with greater ease and 
    scalability.

    \vspace{4pt}
    The tool incorporates a collaborative workflow involving domain 
    experts and ontology engineers. Domain experts contribute their 
    knowledge during the initial stages of domain analysis, 
    conceptualization, and formalization. 

    \vspace{4pt}
    Ontology engineers utilize \DBFO to construct OWL
    ontologies\raise0.7ex\hbox{\tiny{ [8]}} based on the information 
    gathered from domain experts. The tool provides a user-friendly 
    interface for defining classes, properties, and relationships within 
    the ontology. \DBFO ensures that the generated ontologies adhere to 
    the Basic Formal Ontology (BFO) standard, enhancing their
    consistency and interoperability.

    \vspace{4pt}
    The developed ontologies can be exported in  OWL/XML, for use 
    in different applications. Additionally, the tool integrates 
    with a range of ontology visualization and reasoning tools, 
    such as GraphDB, Protégé, and OntoTrek 3D Viewer, enabling 
    users to explore, analyze, and reason with the created ontologies.

    \vspace{4pt}
    \DBFO supports an iterative development process, allowing 
    for continuous refinement and improvement of the ontology. 
    Users can add new relationships, refine existing definitions, 
    and incorporate new knowledge through web-based services.

    \vspace{4pt}
    In summary, \DBFO is a powerful tool that streamlines ontology 
    development by combining the efficiency of a relational database
    with the flexibility and expressiveness of OWL. It empowers domain
    experts and ontology engineers to collaborate effectively and 
    create high-quality, BFO-compliant ontologies for a wide range 
    of applications.

%+
%   New Section 2 
%-

\section
{Adding new relationships, relatives, relations via Web-services}
\vspace{-4pt}\\

    \subsection
    {Dedicated Web services are used to modify and extend the initial DB
    content}

    \vspace{-6pt}

    \begin{itemize}
        \piece{\textbf{Class Annotation Control (CAC):}} 
        {This service enables the modification or creation of 
        annotations associated with classes within the ontology. 
        Furthermore, it facilitates the management of database 
        update and insert commands generated during these 
        modifications.}

        \piece{\textbf{Class Definition Service (CDS):}} 
        {This service empowers users to transform the entire 
        OWL class structure, including modifications to subclass, 
        superclass, and disjoint class relationships. The 
        subsequent generation of individuals within the ontology 
        is then based on this revised class structure, ensuring 
        consistency across the entire knowledge representation.}

        \piece{\textbf{Data Property Definition (DPD):}} 
        {This service enables the creation of data properties 
        and the specification of their attributes, such as 
        subproperty/superproperty relationships, property 
        annotations, and data property types. These data 
        properties can then be assigned to the subject and 
        object entities within the defined triplets.}

        \piece{\textbf{Header Annotation Control (HAC):}} 
        {This service facilitates the optional supplementation 
        of existing header annotations with properties derived 
        from external ontologies, such as those defined in the 
        Dublin Core (dc), Friend-of-a-Friend (foaf), or other 
        relevant vocabularies.}

        \piece{\textbf{Object Property Definition (OPD):}} 
        {This service allows for the creation of new object 
        properties. For each newly created object property, 
        users can specify attributes such as super object 
        properties, inverse object properties, and associated 
        object annotation properties, including the annotation 
        itself, its type, and language.}

        \piece{\textbf{Triplet Definition (TD):}} 
        {This service provides a mechanism for defining the 
        subject-predicate-object relationships within the 
        ontology. Users can specify the entities involved 
        in each triplet, identify the associated data properties, 
        and define the corresponding data property values.}
    \end{itemize}

    \vspace{4pt}
    While the maintenance Web services are not included in the 
    \DBFO software product, two of the most commonly used services 
    (CAC and OPD) are presented here for illustrative purposes. 

    \showFig{./pictures/Fig_DOP.png} % filename to be displayed
            {0.65}                   % width
            { The \textit{Object Property Definition}
            Web service.
            \phantom{------------------------------------------}
            \phantom{-----------}
            }
            {\raggedright}
            % indentation
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            {-8pt}                   % space after
 
    \showFig{./pictures/Fig_CAC.png} % filename to be displayed
            {0.65}                   % width
            { The \textit{Class Annotation Control} Web
            service.
            \phantom{------------------------------------------}
            \phantom{-------------}
            } 
            {\raggedright}
            % indentation
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            {-8pt}                   % space after

    \subsection
    {Class annotations}
 
    \vspace{1pt}
    Class annotations are provided in three languages, further enriched by 
    a referential classification based on \\BFO 1.0 (Basic Formal Ontology).
  
    \showFig{./pictures/Fig_BFOann_1.png} % filename to be displayed
            {0.80}                   % width
            { Class Annotation and BFO reference
            \phantom{------------------------------------------}
            \phantom{----------------------}
            } 
            {\raggedright}
            % indentation
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            {-18pt}                   % space after

    As illustrated in Figure 4, each OWL class in the ontology is linked to the
    corresponding BFO entity, with further details available through the EMBL-EBI 
    OLS. The EMBL-EBI OLS (European Molecular Biology Laboratory, European Bioinformatics
    Institute: Ontology Lookup Service) provides further details on the referenced BFO 
    entity, as depicted in Figure~5: 

    \showFig{./pictures/Fig_BFOann_2.png} % filename to be displayed
            {0.9}                   % width
            { \textbf{EMBL-EBI OLS} BFO reference
            \phantom{------------------------------------------}
            \phantom{--------------------}
            } 
            {\raggedright}           % indentation
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            {-6pt}                   % space after

    \vspace{-10pt}
    The database structure of the \DBFO is depicted on the in Figure 6. The
    design was made with the Exterprise Architect modelling tool. 
    
    \showFig{./pictures/Fig_DBdesign_A_rotated.png} % filename to be displayed
            {1.0}                   % width
            { \DBFO Database Structure (1)
            \phantom{------------------------------------------}
            \phantom{--------------------}
            }  
            {\raggedright}           % indentation
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            {-6pt}                   % horizontal shifting
            {-2pt}                   % space between figure and title
            {-1pt}                   % space after
    
    The \DBFO database structure includes four independent tables that 
    store information such as ontology header and trailer data, as well 
    as elucidations of BFO annotations, as depicted in Figure~7.

    \showFig{./pictures/Fig_DBdesign_b.png} % filename to be displayed
            {0.75}                   % width
            { \DBFO Database Structure (2)
            \phantom{------------------------------------------}
            \phantom{--------------------}
            } 
            {\raggedright}           % indentation
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            {-4pt}                   % space between figure and title
            {-12pt}                  % space after

%+
%   New Section 3
%-
\section
{Future Directions: Enhancing Development with Description Logics}

\vspace{8pt}
    The ongoing development of \DBFO aims to incorporate more 
    advanced features. A key step is the introduction of Description 
    Logics\raise0.8ex\hbox{\tiny{ [2]}} (DLs) to enhance the expressivity and
    formal rigor of the generated ontologies. The initial focus will be on 
    the Attributive Language with Concept Negation ($\mathcal{ALC}$), 
    a foundational Description Logic. However, depending on the complexity 
    of the challenges encountered during development, the implementation may 
    be extended to support the more expressive $\mathcal{SROIQ}$ Description 
    Logic.

    \vspace{4pt}
    DLs provide a structured and well-defined framework for representing
    knowledge. As a subset of First-Order Logic (FOL), DLs offer a 
    balance between expressivity and computational tractability.

    \vspace{4pt}
    To support the integration of DLs, the following challenges need 
    to be addressed:

    \vspace{-4pt}
    \begin{itemize}
        \piece{\textit{User Interface for DL Constructs:}} 
        {Developing user-friendly interfaces for handling 
        DL symbols, including their insertion, editing, and 
        display within the DBFOschemafy environment.}

        \piece{\textit{Basic Syntactic Checking:}} 
        {Implementing basic syntactic checks to ensure the 
        validity of DL expressions entered by users.}

        \piece{\textit{OWL Code Generation from DL Expressions:}} 
        {Generating OWL code from the defined DL expressions, 
        ensuring accurate translation and preserving the 
        intended meaning.}
    \end{itemize}

    \vspace{-2pt}
    By addressing these challenges, \DBFO will evolve 
    into a more powerful and sophisticated tool for 
    building high-quality, formally grounded ontologies.

%+
%   New Section 4
%-
\section
{Software Background}
\vspace{8pt}
The software development environment consists of the following components:

    \vspace{-6pt}
    \begin{itemize}
    \piece{\textit{Operating System:}} {macOS Monterey, (Version 12.5.1) 
    running on an iMac (Retina 5k, 27-inch, Late 2015)}
    
    \vspace{-2pt}
    \piece{\textit{RDB:}} {MySQL Server (Version 8.0.30), MySQL Workbench
    (Version 8.0.31 build 2235049 CE (64 bits) Community)}
    
    \vspace{-2pt}
    \piece{\textit{Java Runtime:}} {Java\raise0.8ex\hbox{\tiny{TM}} 
    SE Runtime Environment (build 13.0.2+8)}
    
    \vspace{-2pt}
    \piece{\textit{Java Virtual Machine:}} {Java
    HotSpot\raise0.8ex\hbox{\tiny{TM}}
    64-Bit Server VM (build 13.0.2+8, mixed mode, sharing)} 
    
    \vspace{-4pt}
    \piece{\textit{Integrated Development Environment:}} {Eclipse IDE for Java
    Developers (includes Incubating components), Version: 2021-12 (4.22.0), 
    Build id: 20211202-1639}
    
    \vspace{-2pt}
    \piece{\textit{Prot\'{e}g\'{e}:}} {Open-source ontology editor and framework 
    for building intelligent systems, Version 5.6.3}
    \end{itemize}
    \vspace{-2pt}
           
%+
%   New Section 5
%-
\section
{DBFOschemafy as a Stand-Alone Application}
\vspace{8pt}\\
    \DBFO is not merely a theoretical concept but a fully 
    functional Java application. To facilitate further research 
    and development, all components of the system are made available 
    to the research community, including the Java source code, data 
    models, and example database content.

    \showFig{./pictures/Fig_CmdLine.png} % filename to be displayed
            {0.62}                   % width
            { \DBFO as a running stand alone application
            \phantom{------------------------------------------}
            \phantom{-----}
            } 
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%   New Section 6
%-
\section
{References}
\vspace{4pt}
    \renewcommand*\labelenumi{[\theenumi]}
    \begin{enumerate}
  
    \densepiece{Robert Arp, Barry Smith, and Andrew D. Spear: Building Ontologies 
                with Basic  Formal Ontology. The MIT Press Cambridge,
                Massachusetts London, England. (2015). Massachusetts Institute
                of Technology. ISBN 978-0-262-52781-1.}
                
     \densepiece{Bader, F., Horrocks, I., Lutz, C., Sattler, Uli.
                (2017). An Introduction to Description Logic. Cambridge
                University Press, ISBN 978-0-521-69542-8.}
                
    \densepiece{Allemang, D.,  Hendler, J. A. (2012). Semantic web for the working
                ontologist effective modeling in RDFS and Owl. Dean Allemang, Hendler. J.A.}

    \densepiece{Arp, R., Smith, B., Spear, A. D. (2015). Building ontologies with
                basic formal ontology. MIT Press}

    \densepiece{Curé, O., Blin, G. (2015). RDF database systems: Triples Storage
                and SPARQL query processing. Morgan Kaufmann}

    \densepiece{DuCharme, B. (2011). Learning Sparql: Querying and updating with SPARQL
                1.1. O’Reilly}

    \vspace{2pt}
    \densepiece{Horridge, M. (2011). A Practical Guide To Building OWL Ontologies
                Using Prot\'{e}g\'{e} 4 and CO-ODE Tools. The University Of Manchester
                Press}

    \densepiece{Owl. OWL - Semantic Web Standards. (n.d.)
                \hypersetup{hidelinks}\url{https://www.w3.org}}

    \end{enumerate}

    \vspace{12pt}
    \small{Online Content}
    \vspace{6pt}\\
    \scriptsize{Any control and source data, extended data, supplementary 
                information, and author details are available electronically.}
    \vspace{4pt}\\
    \begin{minipage}{\columnwidth}
        \renewcommand{\arraystretch}{0.9}
        \begin{tabular}{@{}@{\extracolsep{-10pt}}ll@{}}
        \scriptsize{Base URL:}     &
        \scriptsize{\textcolor[RGB]{0,0,255}{\hypersetup{hidelinks}\url{http://www.edithlaszny.eu/ontology/DBFOschemafy/}}}\\
        \scriptsize{Present paper:}& \scriptsize{\texttt{paper/DBFOschemafy\char`_V\char`_3\char`_001.pdf}}\\
        \scriptsize{LaTeX source:} & \scriptsize{\texttt{paper/DBFOschemafy\char`_V\char`_3\char`_001.tex}}\\
        \scriptsize{Figures:}      & \scriptsize{\texttt{paper/figures/}}\\
        \scriptsize{RDB content:}  & \scriptsize{\texttt{RunnableEnv/*.sql}}\\
        \scriptsize{Java sources:} & \scriptsize{\texttt{eclipseWorkSpacePRINCE2/*}}\\
        \scriptsize{Javadoc:}      & \scriptsize{\texttt{javadoc/index.html}}\\
        \scriptsize{OWL Ontology:} & \scriptsize{\texttt{RunnableEnv/resultOntology/DBFOprince2\char`_ontology.owl}}\\
        \scriptsize{Author's data:}& \scriptsize{\texttt{authorsData/*.pdf}}\\
        \end{tabular}
    \end{minipage}
    
    \vspace{60pt}
    
    \textcolor[RGB]{255,0,0}
    {
        \begin{center}
            \line(1,0){\columnwidth}
        \end{center}
    }
    \vspace{-6pt}
    \tiny{This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.\\
         The author declares no conflicts of interest, including any competitive interests.\\
         This paper has been typeset from a \TeX/\LaTeX \hspace{2pt}file prepared by the author.}
    
\end{document}

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