Integration of Ontology Alignment and Ontology Debugging for Taxonomy Networks

125 Pages·2014·1.38 MB·English

Link¨opingStudiesinScienceandTechnology. ThesisNo. 1644
LicentiateThesis
Integration of Ontology Alignment
and Ontology Debugging for
Taxonomy Networks
by
Valentina Ivanova
DepartmentofComputerandInformationScience
Link¨opingUniversity
SE-58183Link¨oping,Sweden
Link¨oping2014
ThisisaSwedishLicentiate’sThesis
SwedishpostgraduateeducationleadstoaDoctor’sdegreeand/oraLicentiate’sdegree.
ADoctor’sdegreecomprises240ECTScredits(4yearoffull-timestudies).
ALicentiate’sdegreecomprises120ECTScredits.
Copyright(cid:13)c 2014ValentinaIvanova
ISBN978-91-7519-417-2
ISSN0280–7971
PrintedbyLiUTryck2014
URL:http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-102953
Abstract
Semantically-enabled applications, such as ontology-based search and data inte-
gration, take into account the semantics of the input data in their algorithms.
Such applications often use ontologies, which model the application domains in
question,aswellasalignments,whichprovideinformationabouttherelationships
between the terms in the different ontologies.
The quality and reliability of the results of such applications depend directly on
the correctness and completeness of the ontologies and alignments they utilize.
Traditionally, ontology debugging discovers defects in ontologies and alignments
and provides means for improving their correctness and completeness, while on-
tology alignment establishes the relationships between the terms in the different
ontologies, thus addressing completeness of alignments.
This thesis focuses on the integration of ontology alignment and debugging for
taxonomy networks which are formed by taxonomies, the most widely used kind
of ontologies, connected through alignments.
The contributions of this thesis include the following. To the best of our knowl-
edge,wehavedevelopedthefirstapproachandframeworkthatintegrateontology
alignment and debugging, and allow debugging of modelling defects both in the
structureofthetaxonomiesaswellasintheiralignments. Asdebuggingmodelling
defectsrequiresdomainknowledge,wehavedevelopedalgorithmsthatemploythe
domainknowledgeintrinsictothenetworktodetectandrepairmodellingdefects.
Further, a system has been implemented and several experiments with real-world
ontologies have been performed in order to demonstrate the advantages of our
integrated ontology alignment and debugging approach. For instance, in one of
theexperimentswiththewell-knownontologiesandalignmentfromtheAnatomy
track in Ontology Alignment Evaluation Initiative 2010, 203 modelling defects
(concerning incomplete and incorrect information) were discovered and repaired.
This work has been supported by the Swedish National Graduate School in Com-
puterScience(CUGS),theSwedishe-ScienceResearchCenter(SeRC)andVeten-
skapsr˚adet (VR).
v

Acknowledgements
When life brought me to Sweden I had never imagined the wonderful possi-
bilities I would discover. They did not come for granted, though. The path
through the research world is thorny, going up and down, turning at the
most unpredictable moments. I believe I have managed to put those to my
advantage and now I welcome the next challenge.
IamsincerelythankfultomysupervisorProfessorPatrickLambrixwho
has introduced me to the challenging area of ontologies. While working
under his supervision I have improved my calm judgement of circumstances
and, in general, my analytical skills. He provided encouraging and relaxed
workenvironmentandguidedmeduringallstagesofthiswork. Thankyou,
Patrick!
I am especially grateful to Professor Nahid Shahmehri, my second su-
pervisor, who is the main reason for me being at this university. She is the
one who first believed in my research talent and kindly advised me. I am
also thankful to Associate Professor Lena Str¨omb¨ack and David Byers who
made me believe I possess the strength to take this adventure. They have
introduced me to the wonderful world of research.
Thetimeherewouldnothavebeenthatenjoyablewithoutmycolleagues
who make the work environment so friendly. I also thank the people at the
IDA administrative department, and especially Anne, for their timely and
always kind assistance in various administrative issues. I say thank you
to Brittany Shahmehri for proof reading this thesis and providing valuable
remarks.
I am greatly thankful to my family and friends for their unquestion-
ing support and encouragement. Their belief in the successful end of this
adventure has always been driving me forward.
This work would not have been possible without my life partner Pavel.
He shares the sunny and stormy weather with me. Thank you, Pavel, for
your love and for being here!
Valentina Ivanova
January 2014
Link¨oping, Sweden
vii

Contents
1 Introduction 1
1.1 Semantic Web . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Ontologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.1 Ontology alignment . . . . . . . . . . . . . . . . . . . 4
1.2.2 Ontology debugging . . . . . . . . . . . . . . . . . . . 4
1.2.3 Ontology networks . . . . . . . . . . . . . . . . . . . . 5
1.2.4 Benefits from the integration of ontology alignment
and ontology debugging . . . . . . . . . . . . . . . . . 5
1.3 Problem formulation . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.5 Thesis structure. . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6 List of publications . . . . . . . . . . . . . . . . . . . . . . . . 9
1.6.1 Thesis based on. . . . . . . . . . . . . . . . . . . . . . 9
1.6.2 Related publications . . . . . . . . . . . . . . . . . . . 9
1.6.3 Other publications . . . . . . . . . . . . . . . . . . . . 10
2 Background 11
2.1 Ontologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.1 Components . . . . . . . . . . . . . . . . . . . . . . . 12
2.1.2 Classification . . . . . . . . . . . . . . . . . . . . . . . 15
2.1.3 Applications . . . . . . . . . . . . . . . . . . . . . . . 17
2.2 Ontology alignment. . . . . . . . . . . . . . . . . . . . . . . . 17
2.3 Ontology debugging . . . . . . . . . . . . . . . . . . . . . . . 20
2.3.1 Classification of defects . . . . . . . . . . . . . . . . . 21
2.4 Definitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4.1 Ontologies and ontology networks . . . . . . . . . . . 23
2.4.2 Knowledge bases . . . . . . . . . . . . . . . . . . . . . 23
3 Framework and Algorithms 25
3.1 Framework and workflow . . . . . . . . . . . . . . . . . . . . 26
3.2 Methods in the framework . . . . . . . . . . . . . . . . . . . . 28
3.2.1 Detect missing and wrong is-a relations and mappings 28
3.2.2 Repair missing and wrong is-a relations and mappings 31
3.3 Algorithms in the debugging component . . . . . . . . . . . . 35
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CONTENTS
3.3.1 Detect and validate candidate missing is-a relations
and mappings . . . . . . . . . . . . . . . . . . . . . . . 35
3.3.2 Repair missing and wrong is-a relations and mappings 38
3.4 Algorithms in the alignment component . . . . . . . . . . . . 43
3.4.1 Detect and validate candidate missing mappings . . . 43
3.4.2 Repair missing and wrong mappings . . . . . . . . . . 44
3.5 Interactions between the alignment component and the de-
bugging component . . . . . . . . . . . . . . . . . . . . . . . . 45
4 Implemented System 47
4.1 Detectandvalidatecandidatemissingis-arelationsandmap-
pings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.1.1 Detect and validate candidate missing is-a relations . 48
4.1.2 Detect and validate candidate missing mappings . . . 49
4.2 Repair missing and wrong is-a relations and mappings . . . . 51
4.2.1 Repair wrong is-a relations and mappings . . . . . . . 51
4.2.2 Repair missing is-a relations and mappings . . . . . . 52
5 Experiments and Discussions 55
5.1 Ontology debugging . . . . . . . . . . . . . . . . . . . . . . . 55
5.1.1 OAEI Anatomy 2010 . . . . . . . . . . . . . . . . . . . 55
5.2 Integration of ontology debugging and ontology alignment . . 60
5.2.1 OAEI Anatomy 2011 . . . . . . . . . . . . . . . . . . . 60
5.2.2 OAEI Benchmark 2010 . . . . . . . . . . . . . . . . . 64
5.2.3 ToxOntology-MeSH use case . . . . . . . . . . . . . . 70
5.3 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
6 Related work 79
6.1 Ontology debugging . . . . . . . . . . . . . . . . . . . . . . . 79
6.1.1 Debugging modelling defects . . . . . . . . . . . . . . 79
6.1.2 Debugging semantic defects . . . . . . . . . . . . . . . 82
6.2 Ontology alignment. . . . . . . . . . . . . . . . . . . . . . . . 86
6.3 Integration of ontology alignment and ontology debugging . . 88
7 Conclusions and Future Work 91
7.1 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
7.1.1 Debugging of ontologies and alignments . . . . . . . . 92
7.1.2 Benefits from the integration of ontology alignment
and ontology debugging . . . . . . . . . . . . . . . . . 92
7.1.3 Implemented system . . . . . . . . . . . . . . . . . . . 93
7.2 Future work . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
7.2.1 Extending the system . . . . . . . . . . . . . . . . . . 94
7.2.2 Long-term future work . . . . . . . . . . . . . . . . . . 95
x
List of Figures
2.1 (Part of an) Ontology network. . . . . . . . . . . . . . . . . . 13
2.2 Part of the is-a hierarchy in the Wine ontology. . . . . . . . . 14
2.3 Part of the Wine ontology. . . . . . . . . . . . . . . . . . . . . 15
2.4 A general alignment framework. . . . . . . . . . . . . . . . . . 18
2.5 An unsatisfiable concept in the Pizza ontology. . . . . . . . . 22
3.1 Workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.2 Initialization for detection.. . . . . . . . . . . . . . . . . . . . 35
3.3 Initialization for repairing. . . . . . . . . . . . . . . . . . . . . 38
3.4 Algorithm for generating repairing actions for wrong is-a re-
lations and mappings. . . . . . . . . . . . . . . . . . . . . . . 39
3.5 Algorithm for generating repairing actions for missing is-a
relations and mappings. . . . . . . . . . . . . . . . . . . . . . 41
4.1 Generating and validating CMIs. . . . . . . . . . . . . . . . . 49
4.2 Aligning.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
4.3 Repairing wrong is-a relations. . . . . . . . . . . . . . . . . . 51
4.4 Repairing missing is-a relations. . . . . . . . . . . . . . . . . . 53
xi
LIST OF FIGURES
xii