Onyx: A new Canvas-based tool for visualizing biomedical and health ontologies

Ontologies provide formal, machine-readable, and human-interpretable representations of domain knowledge. Therefore, ontologies have come into question with the development of Semantic Web technologies. People who want to use ontologies need an understanding of the ontology, but this understanding is very difficult to attain if the ontology user lacks the background knowledge necessary to comprehend the ontology or if the ontology is very large. Thus, software tools that facilitate the understanding of ontologies are needed. Ontology visualization is an important research area because visualization can help in the development, exploration, verification, and comprehension of ontologies. This paper introduces the design of a new ontology visualization tool, which differs from traditional visualization tools by providing important metrics and analytics about ontology concepts and warning the ontology developer about potential ontology design errors. The tool, called Onyx, also has advantages in terms of speed and readability. Thus, Onyx offers a suitable environment for the representation of large ontologies, especially those used in biomedical and health information systems and those that contain many terms. It is clear that these additional functionalities will increase the value of traditional ontology visualization tools during ontology exploration and evaluation.     

Translating the Foundational Model of Anatomy into OWL

The Foundational Model of Anatomy (FMA) represents the result of manual and disciplined modeling of the structural organization of the human body. It is a tremendous resource in bioinformatics that facilitates sharing of information among applications that use anatomy knowledge. The FMA was developed in Protégé and the Protégé frames language is the canonical representation language for the FMA. We present a translation of the original Protégé frame representation of the FMA into OWL. Our effort is complementary to the earlier efforts to represent FMA in OWL and is focused on two main goals: (1) representing only the information that is explicitly present in the frames representation of the FMA or that can be directly inferred from the semantics of Protégé frames; (2) representing all the information that is present in the frames representation of the FMA, thus producing an OWL representation for the complete FMA. Our complete representation of the FMA in OWL consists of two components: an OWL DL component that contains the FMA constructs that are compatible with OWL DL; and an OWL Full component that imports the OWL DL component and adds the FMA constructs that OWL DL does not allow.     

基于关系数据库的OWL本体构建方法的研究

利用已有的数据资源以自动或半自动方式构建本体是实现语义Web的任务之一.在分析了现有研究成果及不足的基础上,给出了一个比较系统的基于关系数据库的OWL本体构建方法.介绍了如何从关系模式中识别实体、联系、继承关系、聚类关系及基数约束等语义,完成了从关系数据库语义到本体相应部分的转换,通过原型系统的实现验证了该方法的有效性.     

OWL本体建模中约束公理的应用

本体建模的难点在于概念的定义和概念间关系的描述，OWL中的约束公理正好是解决这个难点问题的强有力方法。约束公理是OWL语言中最核心的部分，通过约束公理可以更完整更明确地定义本体模型，使所建立的本体模型能满足最小本体承诺规则。该文以W3C提供的酒本体为例子，结合工程实践，描述了如何利用OWL的约束公理，完善和准确定义本体中的概念。     

Reusing ontologies on the Semantic Web: A feasibility study

Technologies for the efficient and effective reuse of ontological knowledge are one of the key success factors for the Semantic Web. Putting aside matters of cost or quality, being reusable is an intrinsic property of ontologies, originally conceived of as a means to enable and enhance the interoperability between computing applications. This article gives an account, based on empirical evidence and real-world findings, of the methodologies, methods and tools currently used to perform ontology-reuse processes. We study the most prominent case studies on ontology reuse, published in the knowledge-/ontology-engineering literature from the early nineties. This overview is complemented by two self-conducted case studies in the areas of eHealth and eRecruitment in which we developed Semantic Web ontologies for different scopes and purposes by resorting to existing ontological knowledge on the Web. Based on the analysis of the case studies, we are able to identify a series of research and development challenges which should be addressed to ensure reuse becomes a feasible alternative to other ontology-engineering strategies such as development from scratch. In particular, we emphasize the need for a context- and task-sensitive treatment of ontologies, both from an engineering and a usage perspective, and identify the typical phases of reuse processes which could profit considerably from such an approach. Further on, we argue for the need for ontology-reuse methodologies which optimally exploit human and computational intelligence to effectively operationalize reuse processes.     

Learning domain ontologies for semantic Web service descriptions

High quality domain ontologies are essential for successful employment of semantic Web services. However, their acquisition is difficult and costly, thus hampering the development of this field. In this paper we report on the first stage of research that aims to develop (semi-)automatic ontology learning tools in the context of Web services that can support domain experts in the ontology building task. The goal of this first stage was to get a better understanding of the problem at hand and to determine which techniques might be feasible to use. To this end, we developed a framework for (semi-)automatic ontology learning from textual sources attached to Web services. The framework exploits the fact that these sources are expressed in a specific sublanguage, making them amenable to automatic analysis. We implement two methods in this framework, which differ in the complexity of the employed linguistic analysis. We evaluate the methods in two different domains, verifying the quality of the extracted ontologies against high quality hand-built ontologies of these domains.

Our evaluation lead to a set of valuable conclusions on which further work can be based. First, it appears that our method, while tailored for the Web services context, might be applicable across different domains. Second, we concluded that deeper linguistic analysis is likely to lead to better results. Finally, the evaluation metrics indicate that good results can be achieved using only relatively simple, off the shelf techniques. Indeed, the novelty of our work is not in the used natural language processing methods but rather in the way they are put together in a generic framework specialized for the context of Web services.     

The foundational model of anatomy in OWL: Experience and perspectives

We present the method developed for migrating the Foundational Model of Anatomy (FMA) from its representation with frames in Protégé to its logical representation in OWL and our experience in reasoning with it. Despite the extensive use of metaclasses in Protégé, it proved possible to convert the FMA from Protégé into OWL DL, while capturing most of its original features. The conversion relies on a set of translation and enrichment rules implemented with flexible options. Unsurprisingly, reasoning with the FMA in OWL proved to be a real challenge, due to its sheer size and complexity, and raised significant inference problems in terms of time and memory requirements. However, various smaller versions have been successfully handled by Racer. Some inconsistencies were identified and several classes reclassified. The results obtained so far show the advantage of OWL DL over frames and, more generally, the usefulness of DLs reasoners for building and maintaining the large-scale biomedical ontologies of the future Semantic Web.     

Measuring design complexity of semantic web ontologies

Ontology languages such as OWL are being widely used as the Semantic Web movement gains momentum. With the proliferation of the Semantic Web, more and more large-scale ontologies are being developed in real-world applications to represent and integrate knowledge and data. There is an increasing need for measuring the complexity of these ontologies in order for people to better understand, maintain, reuse and integrate them. In this paper, inspired by the concept of software metrics, we propose a suite of ontology metrics, at both the ontology-level and class-level, to measure the design complexity of ontologies. The proposed metrics are analytically evaluated against Weyuker’s criteria. We have also performed empirical analysis on public domain ontologies to show the characteristics and usefulness of the metrics. We point out possible applications of the proposed metrics to ontology quality control. We believe that the proposed metric suite is useful for managing ontology development projects.     

Verifying feature models using OWL

Feature models are widely used in domain engineering to capture common and variant features among systems in a particular domain. However, the lack of a formal semantics and reasoning support of feature models has hindered the development of this area. Industrial experiences also show that methods and tools that can support feature model analysis are badly appreciated. Such reasoning tool should be fully automated and efficient. At the same time, the reasoning tool should scale up well since it may need to handle hundreds or even thousands of features a that modern software systems may have. This paper presents an approach to modeling and verifying feature diagrams using Semantic Web OWL ontologies. We use OWL DL ontologies to precisely capture the inter-relationships among the features in a feature diagram. OWL reasoning engines such as FaCT++ are deployed to check for the inconsistencies of feature configurations fully automatically. Furthermore, a general OWL debugger has been developed to tackle the disadvantage of lacking debugging aids for the current OWL reasoner and to complement our verification approach. We also developed a CASE tool to facilitate visual development, interchange and reasoning of feature diagrams in the Semantic Web environment.     

An ontology in OWL for legal case-based reasoning

The paper gives ontologies in the Web Ontology Language (OWL) for Legal Case-based Reasoning (LCBR) systems, giving explicit, formal, and general specifications of a conceptualisation LCBR. Ontologies for different systems allows comparison and contrast between them. OWL ontologies are standardised, machine-readable formats that support automated processing with Semantic Web applications. Intermediate concepts, concepts between base-level concepts and higher level concepts, are central in LCBR. The main issues and their relevance to ontological reasoning and to LCBR are discussed. Two LCBR systems (AS-CATO, which is based on CATO, and IBP) are analysed in terms of basic and intermediate concepts. Central components of the OWL ontologies for these systems are presented, pointing out differences and similarities. The main novelty of the paper is the ontological analysis and representation in OWL of LCBR systems. The paper also emphasises the important issues concerning the representation and reasoning of intermediate concepts.

Web本体语言OWL

随着对语义Web研究的深入,人们越来越关注在Web上信息内容的表示和检索问题。在语义Web的七层模型中,建立在RDF模式层之上的本体语言层用于形式化描述Web文档中词汇的含义,是建立语义Web的关键环节。该文介绍了W3C最新给出的Web本体语言OWL,给出TOWL3个子语言构造成分的含义说明,并比较了3种子语言间的差别。     

Bridging the gap between OWL and relational databases

Despite similarities between the Web Ontology Language (OWL) and schema languages traditionally used in relational databases, systems based on these languages exhibit quite different behavior in practice. The schema statements in relational databases are usually interpreted as integrity constraints and are used to check whether the data is structured according to the schema. OWL allows for axioms that resemble integrity constraints; however, these axioms are interpreted under the standard first-order semantics and not as checks. This often leads to confusion and is inappropriate in certain data-centric applications. To explain the source of this confusion, in this paper we compare OWL and relational databases w.r.t. their schema languages and basic computational problems. Based on this comparison, we extend OWL with integrity constraints that capture the intuition behind similar statements in relational databases. We show that, if the integrity constraints are satisfied, they need not be considered while answering a broad range of positive queries. Finally, we discuss several algorithms for checking integrity constraint satisfaction, each of which is suitable to different types of OWL knowledge bases.     

基于本体的信息处理系统的设计与实现

语义Web是W3C制定的关于下一代Web技术的一个蓝图。本体作为其中的一部分,将起到非常重要的作用。用于定义和描述Web本体的Web本体语言,尤其是由W3C所设计的OWL,将在其中扮演重要的角色。该文探讨了一个基于本体的信息处理系统的设计和实现,并分析了可扩展性、查询灵活性及逻辑推理等特点。     

Interoperability results for Semantic Web technologies using OWL as the interchange language

Using Semantic Web technologies in complex scenarios requires that such technologies correctly interoperate by interchanging ontologies using the RDF(S) and OWL languages. This interoperability is not straightforward because of the high heterogeneity in Semantic Web technologies and, while the number of such technologies grows, affordable mechanisms for evaluating Semantic Web technology interoperability are needed to comprehend the current and future interoperability of Semantic Web technologies.This paper presents the OWL Interoperability Benchmarking, an international benchmarking activity that involved the evaluation of the interoperability of different Semantic Web technologies using OWL as the interchange language. It describes the evaluation resources used in this benchmarking activity, the OWL Lite Import Benchmark Suite and the IBSE tool, and presents how to use them for evaluating the OWL interoperability of Semantic Web technologies. Moreover, the paper offers an overview of the OWL interoperability results of the eight tools participating in the benchmarking: one ontology-based annotation tool (GATE), three ontology frameworks (Jena, KAON2, and SWI-Prolog), and four ontology development tools (Protégé Frames, Protégé OWL, SemTalk, and WebODE).     

A semantic metrics suite for evaluating modular ontologies

Ontologies, which are formal representations of knowledge within a domain, can be used for designing and sharing conceptual models of enterprises information for the purpose of enhancing understanding, communication and interoperability. For representing a body of knowledge, different ontologies may be designed. Recently, designing ontologies in a modular manner has emerged for achieving better reasoning performance, more efficient ontology management and change handling. One of the important challenges in the employment of ontologies and modular ontologies in modeling information within enterprises is the evaluation of the suitability of an ontology for a domain and the performance of inference operations over it. In this paper, we present a set of semantic metrics for evaluating ontologies and modular ontologies. These metrics measure cohesion and coupling of ontologies, which are two important notions in the process of assessing ontologies for enterprise modeling. The proposed metrics are based on semantic-based definitions of relativeness, and dependencies between local symbols, and also between local and external symbols of ontologies. Based on these semantic definitions, not only the explicitly asserted knowledge in ontologies but also the implied knowledge, which is derived through inference, is considered for the sake of ontology assessment. We present several empirical case studies for investigating the correlation between the proposed metrics and reasoning performance, which is an important issue in applicability of employing ontologies in real-world information systems.     

基于OWL的电厂设备故障特征的知识表示

为了对电力行业复杂的故障信息进行有效的知识管理,本文将本体论方法引入到设备故障信息的知识表示中。利用OWL本体语言的知识表示特性,介绍了基于OWL的电厂设备故障特征知识表示的过程,为特定领域知识的公共一致表示提供了新的思路,本研究结果不仅可以促进电力行业知识的共享和重用,还方便了电力行业内部以及企业间知识管理和信息交换。