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«OBJECT DATABASES AND THE SEMANTIC WEB A THESIS SUBMITTED IN FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY. ING. JAKUB ...»

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BRNO UNIVERSITY OF TECHNOLOGY

FACULTY OF INFORMATION TECHNOLOGY

OBJECT DATABASES

AND THE SEMANTIC WEB

A THESIS SUBMITTED IN FULFILLMENT

OF THE REQUIREMENTS FOR THE DEGREE OF

DOCTOR OF PHILOSOPHY.

ING. JAKUB GÜTTNER

Field of specialization: Information Systems Supervised by: Prof. Ing. Tomáš Hruška, CSc.

State doctoral exam: June 18, 2003 Submitted on: June 31, 2004 Availability: Library of the Faculty of Information Technology, Brno University of Technology, Czech Republic

I would like to give thanks to those who taught me so much:

Dagmar Güttnerová for teaching me to remain steadfast in all I do;

Stanislav and Pavla Güttnerovi for teaching me to learn;

Tomáš Hruška for teaching me to separate the wheat from the chaff;

Alexander Meduna for teaching me the joys of pure research;

and Jesus Christ for teaching me the most important thing, and how to put it all together.

Ing. Jakub Güttner Brno, June 24, 2004

ABSTRACT

This thesis presents the idea of using object-oriented database mechanisms within the Semantic Web, and provides the theoretical foundations that are necessary for this to happen.

The thesis starts with an overview of object-oriented database standards, data models and formal paradigms, followed by an overview of the Semantic Web RDF/S framework, its model-theoretic semantics, current state of art and emerging applications. The idea of the Semantic Web as a worldwide loosely bound database is then explored by comparing the features of object-oriented data models and RDF/S graphs. After outlining their similarities and the advantages of applying several database concepts to the Semantic Web environment, a formal model of an object database on top of RDF/S is presented. This description is followed by several extensions to the core model (object graph navigation, mining objects from RDF/S and implementation notes) and suggestions of future research

KEYWORDS

Object-Oriented Database, Semantic Web, Data Modeling, RDF, RDFS, CDL, ODMG, SODA

ABSTRAKT

Tato disertační práce předkládá myšlenku využití mechanismů objektově orientovaných databází v prostředí sémantického Webu a pokládá teoretické základy nezbytné k dosažení tohoto cíle.

Disertační práce začíná přehledem současného stavu standardů, datových modelů a formálních paradigmat objektově orientovaných databází, a přehledem současného stavu, teoretických východisek a vznikajících aplikací sémantického Webu a modelu RDF/S. Dále je zkoumán sémantický Web z pohledu celosvětové volně vázané databáze a jeho rysy jsou srovnány s principy objektově orientovaných datových modelů. Po analýze jejich podobností a výhod, které by přinesla aplikace některých databázových konceptů do prostředí sémantického Webu, je představen formální model objektové databáze nad sémantickým základem RDF/S. Tento popis je následován několika rozšířeními základního modelu (navigace v objektovém grafu, získávání objektů z RDF/S a implementační poznámky) a návrhem možných směrů dalšího výzkumu.

KLÍČOVÁ SLOVA Objektově orientované databáze, sémantický Web, datové modelování, RDF, RDFS, CDL, ODMG, SODA

TABLE OF CONTENTS

1 INTRODUCTION ___________________________________________________ 1

1.1 Goals of This Thesis__________________________________________________ 2

1.2 Overview of the Thesis________________________________________________ 2

1.3 Typographic Conventions ______________________________________________ 3 2 OVERVIEW OF OBJECT–ORIENTED DATABASES __________________________4

2.1 Object–Oriented Database System Manifesto _______________________________ 5

2.2 The ODMG Standard _________________________________________________ 7

2.3 Java Data Objects — JDO_____________________________________________ 11

2.4 Set Models (O2) ____________________________________________________ 15

2.5 Concept Definition Language — CDL ___________________________________ 18

2.6 Categorical models __________________________________________________ 21

2.7 Logic Models (F–Logic) ______________________________________________ 25 3 OVERVIEW OF THE SEMANTIC WEB __________________________________29

3.2 Model–Theoretic RDF Semantics _______________________________________ 31

3.3 OWL _____________________________________________________________ 35

3.4 Some RDF applications_______________________________________________ 38 4 SEMANTIC WEB AS AN OBJECT DATABASE______________________________43

4.1 Similarities _________________________________________________________ 43

4.2 Sharing Concepts ___________________________________________________ 44

4.3 Data Modeling From a RDF Perspective __________________________________ 45 5 DATABASE MODEL ON TOP OF RDF/S ________________________________48





5.1 Features of the Model ________________________________________________ 48

5.2 Obtaining the OODB Graph __________________________________________ 49

5.3 A Formal Description ________________________________________________ 49

5.4 Example of the SODA Model__________________________________________ 56 6 EXTENDING THE MODEL __________________________________________ 61

6.1 Mining Objects From RDF/S __________________________________________ 61

6.2 Accessing Graph Data________________________________________________ 63

6.3 Implementation Notes________________________________________________ 65 7 CONCLUSION ____________________________________________________66

7.1 Main Contributions __________________________________________________ 66

7.2 Directions for Further Research ________________________________________ 66 A REFERENCES ____________________________________________________68 B OTHER SEMANTIC WEB TOOLS AND APPLICATIONS _____________________72 B.1 LSID in Bioinformatics _______________________________________________ 72 B.2 Sesame ___________________________________________________________ 73 B.3 Haystack __________________________________________________________ 73 B.4 SKOS and SWAD-Europe_____________________________________________ 74 B.5 PRISM ___________________________________________________________ 74 C A SURVEY OF RDF QUERY LANGUAGES _______________________________76 C.1 GetData __________________________________________________________ 76 C.2 RQL _____________________________________________________________ 76 C.3 SeRQL ___________________________________________________________ 77 C.4 RDQL____________________________________________________________ 77 C.5 PerlRDF Queries____________________________________________________ 77 D LIST OF FIGURES__________________________________________________79

–  –  –

There’s so much more that could be done. The reason is, in a word, databases: dusty, musty databases filled with useful data that would be far more useful if linked with other, equally dusty databases; enormous databases that are locked up inside ancient mainframes and quaintly archaic minicomputers; lonely databases residing on specialized file servers throughout an enterprise; even modern databases on Web servers, all dressed up and ready to go, but stuck in long-obsolete proprietary formats or accessible only through hypermodern scripting languages.

Second-generation e-commerce will depend on unlocking those databases.1 Opening up databases to the world and letting them cooperate on solving problems is not a simple task, because seamless integration of massively heterogeneous technologies requires a carefully designed framework of standards, languages and tools. All of these need to be based on rigorous mathematical foundations that define underlying semantics. This thesis aims at working with such foundations for the integration of two technologies that may be important in fulfilling the above goal — the Semantic Web (chapter 4) and object-oriented databases (chapter 3).

Semantic Web is a W3C initiative that provides standards for creating an interoperable, semantically rich, and machine-readable network of information similar to the World Wide Web — it aims to do for computers what the Web has done for humans. Its theoretical foundations lie in the areas of ontologies, knowledge-based and logical programming, and artificial intelligence.

Proposed data structure is very loose, does not differentiate between data and metadata, and allows incomplete or conflicting information.

Object-oriented databases are gaining new popularity with the advent of XML, Web services and business-to-business integration. The leading relational database vendors are now providing object-relational bindings, and both.NET and Java provide object-oriented data management frameworks (ADO.NET, JDO). There is a pressing need to design a unified formalism for the object-oriented data model.

Object-oriented database schemas are much richer than relational ones, and their features come close to ontological languages. Formalizing them with the Semantic Web RDF model theory is the goal of this thesis.

The growing Semantic Web needs to address a number of database issues, such as dynamic behavior, transactions and updates, security and access control, and efficient data storage. Another goal of this thesis is to naturally adapt these concepts from the area object databases.

Object databases can thus gain a widely accepted formal foundation, increased flexibility thanks to the loose format of Semantic Web RDF data, and natural integration with the upcoming Semantic Web.

–  –  –

2.1 GOALS OF THIS THESIS Explore existing object-oriented database standards and models. Give an overview of the Semantic Web and its database-oriented research and applications.

Describe the similarities and differences between elements and constructs of object-oriented data models and the Semantic Web RDF/S model. Outline the advantages of merging these two areas.

Define a formal model of an object-oriented database on top of the RDF/S framework.

Show how some database concepts can be used in context of the RDF/S based Semantic Web.

2.2 OVERVIEW OF THE THESIS Chapter 3, Overview of Object–Oriented Databases, clarifies the modeling paradigm and design choices of object-oriented databases and overviews different standards, languages and models.

Chapter 4, Overview of the Semantic Web, explains why and how the Semantic Web initiative plans to expand the existing World Wide Web. This chapter gives model-theoretic semantics of the RDF/S model and shows examples of existing RDF research and applications.

Chapter 5, Semantic Web as an Object Database, compares the models of object databases, RDF/S graphs, and the models used in human thinking. The chapter lists similarities between the RDF-based Semantic Web and an object database and advocates a RDF/S object model that would constitute a loosely bound worldwide object database. Different database concepts could then be adopted for the Semantic Web.

Chapter 6, Database Model on Top of RDF/S, gives a formal description of an object model on top of RDF model-theoretic semantics. Design choices and limitations of the model are also discussed. This chapter contains a large example of how the model can be used.

Chapter 7, Extending the Model, discusses three aspects of extending the formal model — why and how to extract object structures from raw RDF/S data, how to access and navigate RDFbased object graphs, and how the proposed model could possibly be implemented.

Chapter 8, Conclusion, sums up the contribution of this dissertation and suggests directions for further research.

Appendices include the list of references, an overview of several interesting Semantic Web projects, a brief survey of RDF query languages, a list of figures and a glossary of the most frequent abbreviations in this thesis.

–  –  –

2.3 TYPOGRAPHIC CONVENTIONS



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