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     Open architecture for Accessible Services

     Integration and Standardization - G.A. 215754

    OASIS Open architecture for Accessible

    Services Integration and Standardization

     GRANT AGREEMENT # 215754

    Ontologies, typologies, models and

    management tools

    D1.1.1 Deliverable No.

    SP1 Open system reference SubProject No. SubProject Title

    architecture, user

    interfaces, platform and

    tools

    WP1.1 Benchmarking of Workpackage No. Workpackage Title

    existing ontologies and

    ontology management

    tools

    A1.1.4 Extraction of typologies Activity No. Activity Title

    and models of

    ontologies

    Dionysis Kehagias, Dionysia Kontotasiou, Authors (per company, if more than

    Georgios Mouratidis, Theofilos Nikolaou, one company provide it together)

    Ioannis Papadimitriou (CERTH/ITI) (Please,

    add)

    D Status (F: final; D: draft; RD: revised

    draft):

    OASIS Deliverable D1_1_1_version_1.0.doc File Name:

    01 January 2008, 48 Months Project start date and duration

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    List of Abbreviations

AI Artificial intelligence

    DAML DARPA Agent Markup Language DARPA Defense Advanced Research Projects Agency DL Description Logic

    DTD Document Type Definition

    HTML HyperText Markup Language

    KB Knowledge Base

    KIF Knowledge Interchange Format

    KR Knowledge Representation

    KSL Knowledge Systems Laboratory

    OCML Operational Conceptual Modelling Language OIL Ontology Inference Layer

    OKBC Open Knowledge Base Connectivity OWL Web Ontology Language

    RDF Resource Description Framework SHOE Simple HTML Ontology Extensions XML Extensible Markup Language

    XSD XML Schema Definition

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Table of Contents

    LIST OF ABBREVIATIONS............................................................................................... 2

    TABLE OF CONTENTS ..................................................................................................... 3

    LIST OF FIGURES .............................................................................................................. 6

    LIST OF TABLES ................................................................................................................ 7

    EXECUTIVE SUMMARY................................................................................................... 8

    EXECUTIVE SUMMARY................................................................................................... 8

    1. INTRODUCTION .......................................................................................................... 9

    1.1. OASIS OBJECTIVES .............................................................................................. 10 1.2. DELIVERABLE STRUCTURE .................................................................................... 10 2. EXISTING ONTOLOGIES ......................................................................................... 12

    2.1. NUTRITIONAL ADVISOR ONTOLOGIES .................................................................... 12 2.2. ACTIVITY COACH ONTOLOGIES ............................................................................. 13 2.3. BRAIN AND SKILLS TRAINER ONTOLOGIES ............................................................. 13 2.4. SOCIAL RELATION AND RECREATION ONTOLOGIES ................................................ 13 2.5. HEALTH MONITORING ONTOLOGIES ...................................................................... 14 2.6. ENVIROMENTAL CONTROL ONTOLOGIES ................................................................ 19 2.7. TRANSPORT INFORAMTION ONTOLOGIES ................................................................ 19 2.8. ROUTE GUIDANCE ONTOLOGIES ............................................................................ 21 2.9. PERSONAL MOBILITY ONTOLOGIES ........................................................................ 21 2.10. SMART WORKPLACES ............................................................................................ 24 2.11. OTHER AREAS ....................................................................................................... 24

    3. TYPOLOGY FOR THE CHARACTERISATION OF ONTOLOGIES ................... 26

    3.1. EVALUATION METRICS FOR ONTOLOGIES (UNIBREMEN) ........................................ 26

    3.1.1. Internal: Lexical / Vocabulary layer .................................................................. 27

    3.1.2. Internal: Structural / architectural layer ........................................................... 27

    3.1.3. Internal: Representational / semantic layer ....................................................... 28

    3.1.4. Internal: Data / Application layer ..................................................................... 28

    3.1.5. Internal: Philosophical layer ............................................................................. 29

    3.1.6. External: Usability layer ................................................................................... 29

    3.2. OASIS METHODOLOGICAL APPROACH FOR ONTOLOGY EVALUATION AND

    REFINEMENT BASED ON ARCHITECTURAL AND DESIGN ASPECTS (UNIBREMEN) .................... 30

    3.2.1. Introduction ...................................................................................................... 30

    3.2.2. Reusing Existing Candidate Ontologies ............................................................. 30

    3.2.3. General Restructuring Issues............................................................................. 31

    3.2.4. More Specific Comments and Suggestions on Restructuring .............................. 33

    3.3. A CASE STUDY EXAMPLE: RESTRUCTURING THE ASK-IT ONTOLOGIES .................. 34

    3.3.1. The ASK-IT Ontologies...................................................................................... 34

    3.3.2. The Refinement/Improvement Process ............................................................... 35

    3.4. CONCLUSIONS (CERTH/ITI) ................................................................................. 48 4. ONTOLOGY LANGUAGES ...................................................................................... 49

    4.1. FIRST GENERATION ONTOLOGY LANGUAGES (LST-UPM) ..................................... 49

    4.1.1. KIF and Ontolingua .......................................................................................... 49

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4.1.2. Loom ................................................................................................................. 49

    4.1.3. PowerLoom ....................................................................................................... 50

    4.1.4. OCML ............................................................................................................... 50

    4.1.5. F-Logic ............................................................................................................. 50

    4.1.6. OKBC ............................................................................................................... 50

    4.1.7. SHOE ................................................................................................................ 51

    ASED ONTOLOGY LANGUAGES (LST-UPM) ............................................... 51 4.2. XML-B

    4.2.1. XOL .................................................................................................................. 51

    4.2.2. DAML + OIL .................................................................................................... 51

    4.2.3. RDF .................................................................................................................. 52

    4.2.4. OWL ................................................................................................................. 57

    4.2.5. RacerPro ........................................................................................................... 64

    4.3. THE HETEROGENEOUS TOOL SET (UNIBREMEN) .................................................... 64

    4.3.1. CASL ................................................................................................................. 64

    4.3.2. CoCASL ............................................................................................................ 64

    4.3.3. HasCASL .......................................................................................................... 64

    4.3.4. Haskel ............................................................................................................... 64

    4.3.5. CASL-DL .......................................................................................................... 64

    4.4. ONTOLOGY QUERY LANGUAGES (LST-UPM) ........................................................ 64

    4.4.1. nRQL and Racer................................................................................................ 65

    4.4.2. OWL-QL ........................................................................................................... 65

    4.4.3. RDQL................................................................................................................ 65

    4.4.4. Vampire ............................................................................................................ 66

    4.4.5. SPARQL ............................................................................................................ 66

    4.4.6. WSDL................................................................................................................ 66

    5. OPEN SOURCE ONTOLOGY TOOLS (ANCO, UNIBREMEN, MIZAR) ............. 67

    5.1. PROTÉGÉ 4.0 ALPHA (ANCO) ................................................................................ 67 5.1.1. Main Features ................................................................................................... 67

    5.2. BIOPORTAL (UNIBREMEN) .................................................................................... 79 5.3. OILED (ANCO) .................................................................................................... 79 5.4. APOLLO ................................................................................................................ 81 5.5. RDFEDT ............................................................................................................... 82 5.6. ONTOLINGUA ........................................................................................................ 83 5.7. ONTOEDIT ............................................................................................................ 85 5.8. WEBODE ............................................................................................................. 87 5.9. KAON (MIZAR) .................................................................................................. 88 5.10. ICOM ................................................................................................................... 90

    5.11. DOE (DIFFERENTIAL ONTOLOGY EDITOR) ............................................................. 92

    5.12. WEBONTO ............................................................................................................ 93 5.13. ONTOWIKI ............................................................................................................ 94 5.14. ISAVIZ .................................................................................................................. 95 5.15. HOZO .................................................................................................................. 97

    5.16. GROWL ............................................................................................................... 97 5.17. SEMANTIC WIKIS................................................................................................... 97 5.18. SWOOP ............................................................................................................... 98 6. REASONERS (INFOTRIP) ....................................................................................... 100

    6.1. DESCRIPTION LOGIC REASONERS ......................................................................... 100

    6.1.1. FaCT++ ......................................................................................................... 102

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    6.1.2. RacerPro ......................................................................................................... 103

    6.1.3. Pellet ............................................................................................................... 105

    6.1.4. KAON2 ........................................................................................................... 108

    6.1.5. CEL................................................................................................................. 109

    6.1.6. Cerebra Engine ............................................................................................... 109

    6.1.7. FuzzyDL .......................................................................................................... 110

    6.1.8. QuOnto ........................................................................................................... 110

    ESCRIPTION LOGIC REASONERS WHICH ARE NO LONGER ACTIVELY SUPPORTED... 110 6.2. D

    6.2.1. Classic ............................................................................................................ 110

    6.2.2. Loom ............................................................................................................... 111 6.3. RULE ENGINES .................................................................................................... 111

    6.3.1. Jess ................................................................................................................. 111

    6.3.2. XSB ................................................................................................................. 111

    6.3.3. CWM ............................................................................................................... 111

    6.3.4. RuleML Engine ............................................................................................... 111 7. CONCLUSIONS ........................................................................................................ 113 8. REFERENCES ........................................................................................................... 115 9. ANNEX1 AUTHORING TOOLS COMPARISON TABLE (CERTH/HIT) ........ 119 PART 1 ............................................................................................................................. 119 PART 2 ............................................................................................................................. 120 10. ANNEX2 TOOLS AND ASSOCIATED PROJECTS (ANCO) ............................. 121

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List of Figures

    Figure 1: Social Relation and Community Building Related Taxonomy ................................ 14 Figure 2: Personal Support Services Related Taxonomy ....................................................... 22 Figure 3: Tourism and Leisure Ontology .............................................................................. 23 Figure 4: Examples of concept hierarchy/taxonomy restructuring ......................................... 36 Figure 5: Example of equal domain properties restructuring ................................................. 38 Figure 6: Examples of eliminating duplicates and merging similar definitions ...................... 44 Figure 7: Examples of improving ontology documentation ................................................... 45 Figure 8: Examples of range definition for object properties ................................................. 45 Figure 9: Examples where disjointness condition holds or not .............................................. 46 Figure 10: Examples of satisfying naming conventions ......................................................... 48 Figure 11: An Example RDF Description ............................................................................. 52 Figure 12: Graph representation of the example RDF Description in Figure 11 ..................... 53 Figure 13: An example RDF Description illustrating the use of Containers ........................... 54 Figure 14: An example of ―making Statements about Statements‖ ........................................ 55

    Figure 15: An example description illustrating the use of SubClassOf Property .................... 56 Figure 16: Domain and Range Constraints in RDF description ............................................. 57 Figure 17: Protégé screenshot ............................................................................................... 67

    Figure 18: OWL Viz plug-in ................................................................................................. 69

    Figure 19: DL-Quey Tab ...................................................................................................... 70

    Figure 20: Object Property Description Table ....................................................................... 70 Figure 21: Matrix Views ....................................................................................................... 71

    Figure 22: Cardinality View ................................................................................................. 71

    Figure 23: Existential Tree.................................................................................................... 72

    Figure 24: Excel Importer ..................................................................................................... 73

    Figure 25: Bookmarks .......................................................................................................... 73

    Figure 26: Taxonomy Cut-Paste ........................................................................................... 74 Figure 27: The Protégé Nerd ................................................................................................. 75

    Figure 28: TerMine plug-in ................................................................................................. 76

    Figure 29: OWL Lint ............................................................................................................ 77

    Figure 30: Annotation Search View ..................................................................................... 78 Figure 31: Alternative Annotation View ............................................................................... 78 Figure 32: Change View ....................................................................................................... 79

    Figure 33: OilEd screenshot .................................................................................................. 80

    Figure 34: Main window with loaded ontology in Apollo ..................................................... 81 Figure 35: RDFedt screenshot ............................................................................................... 83

    Figure 36: Screenshot of ontology creation in Ontolingua ..................................................... 84 Figure 37: OntoEdit screenshot ............................................................................................. 85

    Figure 38: WebODE ontology editor .................................................................................... 88 Figure 39: KAON Tool screenshot ....................................................................................... 89 Figure 40: ICOM screenshot ................................................................................................. 90

    Figure 41: ICOM screenshot ................................................................................................. 91

    Figure 42: DOE screenshot ................................................................................................... 92

    Figure 43: Interoperabitily using RDFS and OWL ................................................................ 93 Figure 44: WebOnto screenshot ............................................................................................ 94 Figure 45: Ontowiki Ontology Editor ................................................................................... 95 Figure 46: IsaViz Ontology Editor ........................................................................................ 96 Figure 47: Architecture of Description Logic ...................................................................... 100 CERTH/ITI D1.1.1 vers. 1.0 RESTRICTED

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Figure 48: Pellet architecture .............................................................................................. 107

    Figure 49: Kaon2 architecture ............................................................................................. 108

List of Tables

    Table 1: OWL code for the first example of Figure 4 ............................................................ 37 Table 2: OWL code for properties restructuring of Figure 5 .................................................. 40 Table 3: Examples of similar ontological concepts repetition ................................................ 42 Table 4: Rewriting in CASL the classes of Table 3 ............................................................... 43 Table 5: OWL code for documenting class “Accommodation” of Figure 7 .......................... 45

    Table 6: OWL code for disjoint concepts of Figure 9 ............................................................ 47 Table 7: Recommended XML Schema Data types ................................................................ 63 CERTH/ITI D1.1.1 vers. 1.0 RESTRICTED

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EXECUTIVE SUMMARY

    The goal of this deliverable ("Ontologies, typologies, models and management tools") is to

    identify all possible existing ontologies and ontology management tools that are freely available and review them in terms of: a) interoperability, b) openness, c) easiness to update and maintain, d) market status and penetration. The results of the review in ontologies are analyzed for each application area, such as transport, tourism, personal services, domotics, health services, social services, natural languages and other HCI-related domains.

    Ontology management tools are used by different groups of people for performing diverse tasks. Although each tool provides different functionalities, most of the users just use only one, because they are not able to interchange their ontologies from one tool to another. A major part of the review was to examine interoperability; namely, to examine if ontologies could be interchanged from one ontology management tool to another, so as to benefit from the different functionalities of these tools. Special attention was given to the special needs of elderly people and ontologies that might support such features and also how easy is to add such features as deriving from WP2.1, WP3.1 and WP5.5 (ontology updates).

    This deliverable also concerns the detection of commonalities and differences between the examined ontologies, both on the same domain (application area) and among different domains. More specifically, during and after the finalization of A1.1.2, the set of candidate ontologies were examined in a semi-automatic (automatic parsing and custom tests by experts) manner for common concepts, so as to become the basis to create a new unified ontology. The unified ontology was later enriched with models concerning special needs of elderly people. Special attention was given to interface issues.

    Finally, this activity set out a generic typology of ontologies that characterises any ontology along two sets of dimensions: the first building on concepts discussed in previous EU projects (e.g. WonderWeb), involving 'basic ontological distinctions', such as parthood, connection, constitution, dependence, participation, unity, and causation, and the second bringing in architectural and design issues, such as: formal-informal, structured-unstructured, richly expressive-less richly expressive.

The OASIS innovative solutions are summarized below:

     Selection of a set of existing ontologies for each application domain (transport,

    tourism, social services, etc) after thorough testing and evaluation, so as to form the

    basis for the definition of the OASIS Hyper Ontology.

     Evaluation of ontology management tools, in terms of modularity and reusability.

     Definition of suitable metrics, in order to review and analyze ontologies and tools for

    managing them in terms of practical aspects, such as usability and accessibility (not

    only performance).

     Spotting commonalities and differences between ontologies not only on the same

    domain but in various application areas, thus to assist creating a mechanism for

    combining concepts with the aid of the OASIS Hyper Ontology.

     Definition of a generic typology of ontologies that can characterise any ontology with

    specific detail support for OASIS-relevant domains.

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1. Introduction

    Ontologies have recently received popularity in the area of knowledge management and knowledge sharing, especially after the evolution of the Semantic Web and its supporting technologies. An ontology defines the terms and concepts (meaning) used to describe and represent an area of knowledge. It may be conceived as an explicit specification of a conceptualization that includes a set of objects, their properties and their values along with the describable relationships among them, reflected in a representational vocabulary with which a knowledge-based program represents knowledge.

    One use of ontologies is to externalize a model and make it easier for business applications to share and / or reuse knowledge and improve information navigation and search by using reasoning. Furthermore, the externalization of models facilitates customization of an application without modifying code. In ontologies, definitions associate the names of entities in the universe of discourse (e.g., classes, relations, functions, or other objects) with human-readable text describing what the names mean, and formal axioms that constrain the interpretation and well-formed use of these terms. Formally, ontologies are the statement of a logical theory.

    The issues that should be concerned when dealing with ontologies include:

     Ontology Description Languages, to introduce formal means for representing

    ontologies and their attributes.

     Ontology Authoring Tools to enable the creation and development and storing of new

    ontologies and the modification, editing and refinement of existing ones.

     Java technologies to enable interoperability between Java applications and formal

    ontology description standards, in the form of APIs or tools that support automatic

    Java code generation.

     Ontology Reasoners to infer information that is not explicitly contained within

    ontologies.

    As far as the available ontology description languages are concerned, the W3C (http://www.w3c.org) recommends a number of specifications. Specifically, XML provides a surface syntax for structured documents, but imposes no semantic constraints on the meaning of these documents. XML Schema is a language for restricting the structure of XML documents. RDF (Resource Description Framework) is a language for creating a data model for objects (or "resources") and relations among them, providing a simple semantics for the data model. The data models are represented in XML syntax. RDF Schema is a vocabulary for describing properties and classes of RDF resources, with semantics for generalization hierarchies of such properties and classes. Finally, OWL (Web Ontology Language) adds more vocabulary for describing properties and classes, as well as relations among classes, cardinality, equality, richer typing of properties, and enumerated classes. OWL succeeds the preceding effort of DAML+OIL in this area. In summary, OWL adds facilities for expressing meaning and semantics to XML, RDF, and RDF Schema, and thus it goes beyond these languages in its ability to represent machine-readable content. Apart from the specifications on ontology description languages, supported by the W3C and which have obtained wide acceptance so far, a couple of other third-party efforts on the definition of standards and syntax rules for ontologies have been developed. These include OCML and DCMI. Finally, the Unified Modelling Language (UML) has also been proposed as a means for describing ontologies.

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    An important issue about ontology-related technologies is the existence of suitable integrated authoring tools for the creation, development and editing of ontologies. A big number of such tools have been developed lately that support various input and output formats with similar or different attributes. In this report the 18 most popular and accepted ontology authoring tools are presented.

1.1. OASIS Objectives

    The overall aim of OASIS is to develop an open and innovative reference architecture, based upon ontologies and semantic services, that will allow plug and play and cost-effective interconnection of existing and new services in all domains required for the independent and autonomous living of the elderly and their Quality of Life enhancement. Both the open reference architecture and the related tools will be made available as open source.

    Within SP1, the innovative new reference architecture is built (called COF: Common Ontological Framework), together with the key tools for its application, such as the ontology application GUI and content connection tools, the necessary AMI framework and agents, the HCI interaction prototyping tool for UI self-adaptation and personalisation and, finally, the instantiation of the overall architecture to the project applications. The reference architecture and tools will all be made available as open source for maximal impact on development practice.

    Within WP1.1 currently available ontologies and comparable methods, relevant for OASIS application scenarios, are firstly extensively benchmarked and used as a requirements specification for the new OASIS architecture. Recent work in the ontological engineering community (Ontolog Summit, April 2007) has produced a preliminary classification of ontologies along the following dimensions: 1. Expressiveness, 2. Structure, 3. Granularity, 4. Intended Use, 5. Automated Reasoning, 6. Prescriptive vs. Descriptive, 7. Governance.

Thus, this deliverable aims:

     To select a set of existing ontologies for each application domain (transport, tourism,

    social services, etc) after thorough testing and evaluation, so as to form the basis for

    the definition of the OASIS Hyper Ontology.

     To evaluate interfaces of ontology management tools, in terms of modularity and

    reusability.

     To benchmark the interoperability of ontology management tools.

1.2. Deliverable Structure

The deliverable is organized as follows:

     In Chapter 2, the existing ontologies are presented.

     Chapter 3 provides a typology for the characterisation of ontologies.

     Chapter 4 presents the existing ontology languages.

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