An Introduction to Ontology Engineering C. Maria Keet

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An Introduction to Ontology Engineering C. Maria Keet
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Contents

Preface vii
How to use the book ix
0.1 Aims and Synopsis . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
0.2 Content at a glance . . . . . . . . . . . . . . . . . . . . . . . . . . . x
0.3 Assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
1 Introduction 1
1.1 What does an ontology look like? . . . . . . . . . . . . . . . . . . . 2
1.2 What is an ontology? . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.1 The definition game . . . . . . . . . . . . . . . . . . . . . . 4
1.2.2 Some philosophical notes on ontologies . . . . . . . . . . . . 7
1.2.3 Good, not so good, and bad ontologies . . . . . . . . . . . . 8
1.3 What is the usefulness of an ontology? . . . . . . . . . . . . . . . . 9
1.3.1 Data and information system integration . . . . . . . . . . . 9
1.3.2 Ontologies as part of a solution to other problems . . . . . . 14
1.3.3 Success stories . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.4 Outline and usage of the book . . . . . . . . . . . . . . . . . . . . . 20
1.5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.6 Literature and reference material . . . . . . . . . . . . . . . . . . . 22
I Logic foundations for ontologies 23
2 First order logic and automated reasoning in a nutshell 25
2.1 First order logic syntax and semantics . . . . . . . . . . . . . . . . 25
2.1.1 Syntax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.1.2 Semantics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.2 Reasoning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.2.2 Basic idea . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
2.2.3 Deduction, abduction, and induction . . . . . . . . . . . . . 36
2.2.4 Proofs with tableaux . . . . . . . . . . . . . . . . . . . . . . 37
2.3 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.4 Literature and reference material . . . . . . . . . . . . . . . . . . . 43
3 Description Logics 45
3.1 DL primer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.1.1 Basic building blocks of DL ontologies . . . . . . . . . . . . 47
3.1.2 Constructors for concepts and roles . . . . . . . . . . . . . . 49
3.1.3 Description Logic semantics . . . . . . . . . . . . . . . . . . 53
3.2 Important DLs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.2.1 A basic DL to start with: ALC . . . . . . . . . . . . . . . . 56
3.2.2 The DL SROIQ . . . . . . . . . . . . . . . . . . . . . . . . 58
3.2.3 Important fragments of SROIQ . . . . . . . . . . . . . . . 59
3.3 Reasoning services . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
3.3.1 Standard reasoning services . . . . . . . . . . . . . . . . . . 61
3.3.2 Techniques: a tableau for ALC . . . . . . . . . . . . . . . . 63
3.4 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.5 Literature and reference material . . . . . . . . . . . . . . . . . . . 65
4 The Web Ontology Language OWL 2 67
4.1 Standardizing an ontology language . . . . . . . . . . . . . . . . . . 68
4.1.1 Historical notes . . . . . . . . . . . . . . . . . . . . . . . . . 68
4.1.2 The OWL 1 family of languages . . . . . . . . . . . . . . . . 70
4.2 OWL 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.2.1 New OWL 2 features . . . . . . . . . . . . . . . . . . . . . . 74
4.2.2 OWL 2 Profiles . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.2.3 OWL 2 syntaxes . . . . . . . . . . . . . . . . . . . . . . . . 77
4.2.4 Complexity considerations for OWL . . . . . . . . . . . . . . 79
4.3 OWL in context . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
4.3.1 OWL and the Semantic Web . . . . . . . . . . . . . . . . . . 81
4.3.2 The Distributed ontology, model, and specification language
DOL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.3.3 Common Logic . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.4 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.5 Literature and reference material . . . . . . . . . . . . . . . . . . . 87
II Developing good ontologies 89
5 Methods and Methodologies 91
5.1 Methodologies for ontology development . . . . . . . . . . . . . . . 92
5.1.1 Macro-level development methodologies . . . . . . . . . . . . 93
5.1.2 Micro-level development . . . . . . . . . . . . . . . . . . . . 97
5.2 Methods to improve an ontology’s quality . . . . . . . . . . . . . . 101
5.2.1 Logic-based methods: explanation and justification . . . . . 101
iv
5.2.2 Philosophy-based methods: OntoClean to correct a taxonomy 103
5.2.3 Combining logic and philosophy: role hierarchies . . . . . . . 104
5.2.4 Heuristics: OntOlogy Pitfall Scanner OOPS! . . . . . . . . . 106
5.2.5 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
5.3 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.4 Literature and reference material . . . . . . . . . . . . . . . . . . . 113
6 Top-down Ontology Development 115
6.1 Foundational ontologies . . . . . . . . . . . . . . . . . . . . . . . . . 115
6.1.1 Typical content of a foundational ontology . . . . . . . . . . 117
6.1.2 Several foundational ontologies . . . . . . . . . . . . . . . . 121
6.1.3 Using a foundational ontology . . . . . . . . . . . . . . . . . 124
6.2 Part-whole relations . . . . . . . . . . . . . . . . . . . . . . . . . . 130
6.2.1 Mereology . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
6.2.2 Modelling and reasoning in the context of ontologies . . . . . 132
6.3 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.4 Literature and reference material . . . . . . . . . . . . . . . . . . . 138
7 Bottom-up Ontology Development 139
7.1 Relational databases and related ‘legacy’ KR . . . . . . . . . . . . . 140
7.2 From spreadsheets to OWL . . . . . . . . . . . . . . . . . . . . . . 144
7.3 Thesauri . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
7.3.1 Converting a thesaurus into an ontology . . . . . . . . . . . 146
7.3.2 Avoiding ontologies with SKOS . . . . . . . . . . . . . . . . 148
7.4 Text processing to extract content for ontologies . . . . . . . . . . . 148
7.5 Other semi-automated approaches . . . . . . . . . . . . . . . . . . . 150
7.6 Ontology Design Patterns . . . . . . . . . . . . . . . . . . . . . . . 152
7.7 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
7.8 Literature and reference material . . . . . . . . . . . . . . . . . . . 159
III Advanced topics in ontology engineering 161
8 Ontology-Based Data Access 165
8.1 Introduction: Motivations . . . . . . . . . . . . . . . . . . . . . . . 166
8.2 OBDA design choices . . . . . . . . . . . . . . . . . . . . . . . . . . 167
8.3 An OBDA Architecture . . . . . . . . . . . . . . . . . . . . . . . . . 168
8.4 Principal components . . . . . . . . . . . . . . . . . . . . . . . . . . 170
8.5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
8.6 Literature and reference material . . . . . . . . . . . . . . . . . . . 175
9 Ontologies and natural languages 177
9.1 Toward multilingual ontologies . . . . . . . . . . . . . . . . . . . . . 178
9.1.1 Linking a lexicon to an ontology . . . . . . . . . . . . . . . . 178
9.1.2 Multiple natural languages . . . . . . . . . . . . . . . . . . . 180
9.2 Ontology verbalisation . . . . . . . . . . . . . . . . . . . . . . . . . 183
9.2.1 Template-based approach . . . . . . . . . . . . . . . . . . . 184
v
9.2.2 Reusing the results for related activities . . . . . . . . . . . 186
9.3 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
9.4 Literature and reference material . . . . . . . . . . . . . . . . . . . 187
10 Advanced Modelling with Additional Language Features 189
10.1 Uncertainty and vagueness . . . . . . . . . . . . . . . . . . . . . . . 189
10.1.1 Fuzzy ontologies . . . . . . . . . . . . . . . . . . . . . . . . . 190
10.1.2 Rough ontologies . . . . . . . . . . . . . . . . . . . . . . . . 193
10.2 Time and Temporal Ontologies . . . . . . . . . . . . . . . . . . . . 197
10.2.1 Why temporal ontologies? . . . . . . . . . . . . . . . . . . . 198
10.2.2 Temporal DLs . . . . . . . . . . . . . . . . . . . . . . . . . . 199
10.3 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
10.4 Literature and reference material . . . . . . . . . . . . . . . . . . . 204
Bibliography 207
A Assignments 227
A.1 Practical Assignment: Develop a Domain Ontology . . . . . . . . . 228
A.2 Project Assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
A.2.1 Suggested set-up of the assignment . . . . . . . . . . . . . . 230
A.2.2 Topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
B OWL 2 Profiles features list 235
C Complexity recap 239
D Answers of selected exercises 243
About the author 255

Preface

This book is my attempt at providing the first textbook for an introduction in ontology
engineering. Indeed, there are books about ontology engineering, but they
either promote one specific ontology or methodology only, are handbooks, or are
conference proceedings. There have been collaborative initiatives that aimed for a
generic introduction, yet they have not made it to the writing stage. Problems to
overcome with such an endeavour—aside from the difficult task of finding time to
write it—are, mainly, to answer the questions of 1) which topics should an introductory
textbook on ontology engineering cover? and 2) how comprehensive should
an introduction be? The answer to the first question is different for the different
audiences, in particular with respect to emphases of one topic or another and the
order of things. The intended audience for this textbook are people at the level of
advanced undergraduate and early postgraduate studies in computer science. This
entails, for instance, that I assume the reader will know what UML class diagrams
and databases are. As computing degrees seem to have a tendency to have become
less theoretical, a solid background in logic, reasoning, and computational
complexity is not expected, so a gentle introduction (or recap, as it may be) of the
core concepts is provided. There are no lengthy philosophical debates in any of the
chapters, but philosophical aspects are presented and discussed mainly only insofar
as they are known to affect the engineering side. There still will be sections of
interest for philosophers and domain experts, but they may prefer to work through
the chapters in a different order (see ‘how to use the book’).
As to how comprehensive an introduction to ontology engineering should be,
there is no good answer. At least for this first version, the aim is for a semester-long
course, where each chapter can be covered in a week and does not requite too much
reading of core material, with the core material being the contents of the chapter.
For an introductory course at undergraduate level, the citations in the text may
be ignored, but it serves to read 1-3 scientific papers per chapter for more detail,
especially if this book is used in a postgraduate course. This makes also sense in
the light that ontology engineering is still an active field of research—hence, some
basics may change still—and it allows for flexibility in a course programme so as
to emphasise one topic more than another, as the lecturer may prefer. The in-text
references also may help students to start reading scientific papers when they are
working on their assignments, as a place to start the consultation of the literature.
I hope I have succeeded in striking a good balance on topics & depth in the first
two blocks of the textbook. Suggestions for improvement are welcome. (Knowing
that ontologists can be a quite critical group, perhaps I should add to that: antes
de criticarme, intenta superarme, i.e., before you criticise me, try to do a better
job at writing an ontology engineering textbook than me.)
The contents of the textbook was written by gradually improving, extending,
and further updating material that started with blog posts in 2009 for the European
Masters in Computational Logic’s Semantic Web Technologies course I taught at
the Free University of Bozen-Bolzano, Italy, in 2009/2010, with the hope of generating
and facilitating online discussions. That failed miserably, but the posts were
visited often. The blogposts were reworked into short syllabi for the Ontology Engineering
courses at the University of Havana and University of Computer Science,
Cuba, in 2010 and at the Masters Ontology Winter School 2010 in South Africa,
which, in turn, were reworked into the COMP718/720 lecture notes at the University
of KwaZulu-Natal and the Ontology Engineering honours course lecture notes
at the University of Cape Town, South Africa, of which the latest version was in
2015. All those chapters have been updated for this textbook, new material added,
and course-specific data has been removed. I had put a CC BY-NC-SA licence on
those 2015 lecture notes, so therefore this book has that Creative Commons licence
as well. If you think this sounds problematic: it probably is not; if in doubt, please
contact me.
Some contents of this book or associated exercises are adapted from slides or
tutorials made by other people, and I would like to thank them for having made
that material available for use and reuse. They are (in alphabetic order) Jos de
Bruijn, Diego Calvanese, Nicola Guarino, Matthew Horridge, Ian Horrocks, Markus
Kr¨otzsch, Tommie Meyer, Mariano Rodr´ıguez-Muro, Frantiˇsek Simanˇc´ık, Umberto
Straccia, and David Toman. I also would like to thank the students who were
enrolled in any of the aforementioned courses, who provided feedback on the blog
posts and lecture notes, and assisted me in fine-tuning where more or less explanations
and exercises were deemed useful.
For the rest, it was a lot of hard work, with a few encouragements by some
academics who appreciated sections of the lecture notes (thank you!) and some
I-ignore-that-advice by others who told me it’s a waste of time because one cannot
score brownie points with a textbook anyway. The most enjoyable of all the
sessions of updating the contents was the increment from the 2015 lecture notes to
the first full draft of the textbook, which was at Consuelo’s casa particular in La
Habana in June 2018 and interspersed with a few casino (salsa) lessons to stretch
the legs and get-togethers with acquaintances and colleagues.