Ontology Evolution: Not the Same as Schema Evolution

As ontology development becomes a more ubiquitous and collaborative process, ontology versioning and evolution becomes an important area of ontology research. The many similarities between database-schema evolution and ontology evolution will allow us to build on the extensive research in schema evolution. However, there are also important differences between database schemas and ontologies. The differences stem from different usage paradigms, the presence of explicit semantics and different knowledge models. A lot of problems that existed only in theory in database research come to the forefront as practical problems in ontology evolution. These differences have important implications for the development of ontology-evolution frameworks: The traditional distinction between versioning and evolution is not applicable to ontologies. There are several dimensions along which compatibility between versions must be considered. The set of change operations for ontologies is different. We must develop automatic techniques for finding similarities and differences between versions.     

A high-level electrical energy ontology with weighted attributes

One of the significant application areas of domain ontologies is known to be text analysis applications like information extraction and text classification systems, and semantic portals. In this paper, we present a high-level ontology for the electrical energy domain. This domain ontology has weighted attributes to cover the inherent fuzziness in the textual representations of its concepts. Additionally, we have included in the ontology the necessary attributes to align the ontology concepts to on-line collaborative knowledge bases like Wikipedia and linked open data sources like DBpedia, other attributes to facilitate its use in multilingual applications, and concepts to hold the named entities in the domain. The ultimate ontology is aligned with the previously proposed ontologies for the energy-related subdomains after extending the latter ones with weighted attributes. We make the ultimate form of the electrical energy ontology, as well as the extended versions of the domain ontologies for the subdomains, available for research purposes. Also included in the paper are sample text analysis applications which mainly exploit the weighted attributes within the ontology.     

Extracting a justification for OWL ontologies by critical axioms

Extracting justifications for web ontology language (OWL) ontologies is an important mission in ontology engineering. In this paper, we focus on black-box techniques which are based on ontology reasoners. Through creating a recursive expansion procedure, all elements which are called critical axioms in the justification are explored one by one. In this detection procedure, an axiom selection function is used to avoid testing irrelevant axioms. In addition, an incremental reasoning procedure has been proposed in order to substitute series of standard reasoning tests w.r.t. satisfiability. It is implemented by employing a pseudo model to detect “obvious” satisfiability directly. The experimental results show that our proposed strategy for extracting justifications for OWL ontologies by adopting incremental expansion is superior to traditional Black-box methods in terms of efficiency and performance.     

Ontology evolution without tears

The evolution of ontologies is an undisputed necessity in ontology-based data integration. Yet, few research efforts have focused on addressing the need to reflect the evolution of ontologies used as global schemata onto the underlying data integration systems. In most of these approaches, when ontologies change their relations with the data sources, i.e., the mappings, are recreated manually, a process which is known to be error-prone and time-consuming. In this paper, we provide a solution that allows query answering in data integration systems under evolving ontologies without mapping redefinition. This is achieved by rewriting queries among ontology versions and then forwarding them to the underlying data integration systems to be answered. To this purpose, initially, we automatically detect and describe the changes among ontology versions using a high level language of changes. Those changes are interpreted as sound global-as-view (GAV) mappings, and they are used in order to produce equivalent rewritings among ontology versions. Whenever equivalent rewritings cannot be produced we a) guide query redefinition or b) provide the best “over-approximations”, i.e., the minimally-containing and minimally-generalized rewritings. We prove that our approach imposes only a small overhead over traditional query rewriting algorithms and it is modular and scalable. Finally, we show that it can greatly reduce human effort spent since continuous mapping redefinition is no longer necessary.     

Ontology versioning in an ontology management framework

Ontologies have become ubiquitous in information systems. They constitute the semantic Web's backbone, facilitate e-commerce, and serve such diverse application fields as bioinformatics and medicine. As ontology development becomes increasingly widespread and collaborative, developers are creating ontologies using different tools and different languages. These ontologies cover unrelated or overlapping domains at different levels of detail and granularity. A uniform framework, which we present here, helps users manage multiple ontologies by leveraging data and algorithms developed for one tool in another. For example, by using an algorithm we developed for structural evaluation of ontology versions, this framework lets developers compare different ontologies and map similarities and differences among them. Multiple-ontology management includes these tasks: maintain ontology libraries, import and reuse ontologies, translate ontologies from one formalism to another, support ontology versioning, specify transformation rules between different ontologies and version, merge ontologies, align and map between ontologies, extract an ontology's self-contained parts, support inference across multiple ontologies, support query across multiple ontologies.     

Addressing the Ontology Acquisition Bottleneck Through Reverse Ontological Engineering

The use of ontologies in knowledge engineering arose as a solution to the difficulties associated with acquiring knowledge, commonly referred to as the knowledge acquisition bottleneck. The knowledge-level model represented in an ontology provides a much more structured and principled approach compared with earlier transfer-of-symbolic-knowledge approaches but brings with it a new problem, which can be termed the ontology-acquisition (and maintenance) bottleneck. Each ontological approach offers a different structure, different terms and different meanings for those terms. The unifying theme across approaches is the considerable effort associated with developing, validating and connecting ontologies. We propose an approach to engineering ontologies by retrospectively and automatically discovering them from existing data and knowledge sources in the organization. The method offered assists in the identification of similar and different terms and includes strategies for developing a shared ontology. The approach uses a human-centered, concept-based knowledge processing technique, known as formal concept analysis, to generate an ontology from examples. To assist classification of examples and to identify the salient features of the example, we use a rapid and incremental knowledge acquisition and representation technique, known as ripple-down rules. The method can be used as an alternative or complement to other approaches.     

Overcoming the pitfalls of ontology authoring: Strategies and implications for tool design

The process of authoring ontologies appears to be fragmented across several tools and workarounds, and there exists no well accepted framework for common authoring tasks such as exploring ontologies, comparing versions, debugging, and testing. This lack of an adequate and seamless tool chain potentially hinders the broad uptake of ontologies, especially OWL, as a knowledge representation formalism. We start to address this situation by presenting insights from an interview-based study with 15 ontology experts. We uncover the tensions that may emerge between ontology authors including antagonistic ontology building styles (definition-driven vs. manually crafted hierarchies). We identify the problems reported by the ontology authors and the strategies they employ to solve them. These data are mapped to a set of key design recommendations, which should inform and guide future efforts for improving ontology authoring tool support, thus opening up ontology authoring to a new generation of users. We discuss future research avenues in light of these results.     

Supporting concurrent ontology development: Framework, algorithms and tool

We propose a novel approach to facilitate the concurrent development of ontologies by different groups of experts. Our approach adapts Concurrent Versioning, a successful paradigm in software development, to allow several developers to make changes concurrently to an ontology. Conflict detection and resolution are based on novel techniques that take into account the structure and semantics of the ontology versions to be reconciled by using precisely-defined notions of structural and semantic differences between ontologies and by extending state-of-the-art ontology debugging and repair techniques. We also present ContentCVS, a system that implements our approach, and a preliminary empirical evaluation which suggests that our approach is both computationally feasible and useful in practice.     

The PROMPT suite: interactive tools for ontology merging and mapping

Researchers in the ontology-design field have developed the content for ontologies in many domain areas. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. We developed a suite of tools for managing multiple ontologies. These suite provides users with a uniform framework for comparing, aligning, and merging ontologies, maintaining versions, translating between different formalisms. Two of the tools in the suite support semi-automatic ontology merging: P is an interactive ontology-merging tool that guides the user through the merging process, presenting him with suggestions for next steps and identifying inconsistencies and potential problems. A P uses a graph structure of ontologies to find correlation between concepts and to provide additional information for P .     

Efficient retrieval of ontology fragments using an interval labeling scheme

Nowadays very large domain ontologies are being developed in life-science areas like Biomedicine, Agronomy, Astronomy, etc. Users and applications can benefit enormously from these ontologies in very different tasks, such as visualization, vocabulary homogenizing and data classification. However, due to their large size, they are often unmanageable for these applications. Instead, it is necessary to provide small and useful fragments of these ontologies so that the same tasks can be performed as if the whole ontology is being used. In this work we present a novel method for efficiently indexing and generating ontology fragments according to the user requirements. Moreover, the generated fragments preserve relevant inferences that can be made with the selected symbols in the original ontology. Such a method relies on an interval labeling scheme that efficiently manages the transitive relationships present in the ontologies. Additionally, we provide an interval’s algebra to compute some logical operations over the ontology concepts. We have evaluated the proposed method over several well-known biomedical ontologies. Results show very good performance and scalability, demonstrating the applicability of the proposed method in real scenarios.     

The International Society for the Study of Vascular Anomalies (ISSVA) ontology

The International Society for the Study of Vascular Anomalies (ISSVA) provides a classification for vascular anomalies that enables specialists to unambiguously classify diagnoses. This classification is only available in PDF format and is not machine-readable, nor does it provide unique identifiers that allow for structured registration. In this paper, we describe the process of transforming the ISSVA classification into an ontology. We also describe the structure of this ontology, as well as two applications of the ontology using examples from the domain of rare disease research. We used the expertise of an ontology expert and clinician during the development process. We semi-automatically added mappings to relevant external ontologies using automated ontology matching systems and manual assessment by experts. The ISSVA ontology should contribute to making data for vascular anomaly research more Findable, Accessible, Interoperable, and Reusable (FAIR). The ontology is available at https://bioportal.bioontology.org/ontologies/ISSVA.     

基于机器学习的本体概念相似性研究

现有的知识系统使用的是集中式的、一致性的、可扩充的Ontology库,不同本体间的语义匹配是语义网发展面临的最富挑战性的问题之一。本文针对领域中存在不同的Ontology的问题,讨论了一种基于多策略机器学习的Ontology匹配方法,重点分析了本体概念的相似度计算,并提出了一种相似度测量算法。     

Supporting ontology adaptation and versioning based on a graph of relevance

Ontologies recently have become a topic of interest in computer science since they are seen as a semantic support to explicit and enrich data-models as well as to ensure interoperability of data. Moreover, supporting ontology adaptation becomes essential and extremely important, mainly when using ontologies in changing environments. An important issue when dealing with ontology adaptation is the management of several versions. Ontology versioning is a complex and multifaceted problem as it should take into account change management, versions storage and access, consistency issues, etc. The purpose of this paper is to propose an approach and tool for ontology adaptation and versioning. A series of techniques are proposed to ‘safely’ evolve a given ontology and produce a new consistent version. The ontology versions are ordered in a graph according to their relevance. The relevance is computed based on four criteria: conceptualisation, usage frequency, abstraction and completeness. The techniques to carry out the versioning process are implemented in the Consistology tool, which has been developed to assist users in expressing adaptation requirements and managing ontology versions.     

A Rule-Based Object-Oriented OWL Reasoner

In this paper, we describe O-DEVICE, a memory-based knowledge-based system for reasoning and querying OWL ontologies by implementing RDF/OWL entailments in the form of production rules in order to apply the formal semantics of the language. Our approach is based on a transformation procedure of OWL ontologies into an object-oriented schema and the application of inference production rules over the generated objects in order to implement the various semantics of OWL. In order to enhance the performance of the system, we introduce a dynamic approach of generating production rules for ABOX reasoning and an incremental approach of loading ontologies. O-DEVICE is built over the CLIPS production rule system, using the object-oriented language COOL to model and handle ontology concepts and RDF resources. One of the contributions of our work is that we enable a well-known and efficient production rule system to handle OWL ontologies. We argue that although native OWL rule reasoners may process ontology information faster, they lack some of the key features that rule systems offer, such as the efficient manipulation of the information through complex rule programs. We present a comparison of our system with other OWL reasoners, showing that O-DEVICE can constitute a practical rule environment for ontology manipulation.     

Comparing relationships in conceptual modeling: mapping to semantic classifications

Much of the research that deals with understanding the real world and representing it in a conceptual model uses some form of the entity-relationship model as a means of representation. This research proposes an ontology for classifying relationship verb phrases based upon the domain and context of the application within which the relationship appears. The classification categories to which the verb phrases are mapped were developed based upon prior research in databases, ontologies, and linguistics. The usefulness of the ontology for comparing relationships when used in conjunction with an entity ontology is discussed. Together, these ontologies can be effective in comparing two conceptual database designs for integration and validation. Empirical testing of the ontology on a number of relationships from different application domains and contexts illustrates the usefulness of the research.     

面向Web信息资源的领域本体模型自动构建机制的研究

领域本体的构建是本体工程研究与应用的重要内容。面向网络Web信息资源,获取领域相关文本信息,通过对文本的概念分析,构建领域本体模型。提出一套本体自动构建机制,该本体构建基于数据挖掘和机器学习技术,内容主要包括基于贝叶斯(Bayes)分类原理;提出多个分类器方式的概念分类过程和算法;提出概念关联分析和概念自学习算法,建立本体原型;提出面向OWL本体模型的转换映射机制,构建基于OWL的本体模型。此外,还提出了从网络资源获取、领域本体建模到本体实施应用的一套完整的本体构建和应用实施的解决方案。     

Integrating ontological modelling and Bayesian inference for pattern classification in topographic vector data

This paper presents an ontology-driven approach for spatial database enrichment in support of map generalisation. Ontology-driven spatial database enrichment is a promising means to provide better transparency, flexibility and reusability in comparison to purely algorithmic approaches. Geographic concepts manifested in spatial patterns are formalised by means of ontologies that are used to trigger appropriate low level pattern recognition techniques. The paper focuses on inference in the presence of vagueness, which is common in definitions of spatial phenomena, and on the influence of the complexity of spatial measures on classification accuracy. The concept of the English terraced house serves as an example to demonstrate how geographic concepts can be modelled in an ontology for spatial database enrichment. Owing to their good integration into ontologies, and their ability to deal with vague definitions, supervised Bayesian inference is used for inferring complex concepts. The approach is validated in experiments using large vector datasets representing buildings of four different cities. We compare classification results obtained with the proposed approach to results produced by a more traditional ontology approach. The proposed approach performed considerably better in comparison to the traditional ontology approach. Besides clarifying the benefits of using ontologies in spatial database enrichment, our research demonstrates that Bayesian networks are a suitable method to integrate vague knowledge about conceptualisations in cartography and GIScience.     

Cluster-Merge本体构造算法

本体构造就是利用各种数据源以半自动方式新建或扩充改编已有本体以构建一个新本体。现有的本体构造方法大都以大量领域文本和背景语料库为基础抽取大量概念术语,然后从中选出领域概念构造出一个本体。Cluster-Merge算法首先对领域文档先用k-means聚类算法进行聚类,然后根据文档聚类的结果来构造本体,最后根据本体相似度进行本体合并得到最终的输出本体。通过实验可证明用Cluster-Merge算法得出的本体可以提高查全率、查准率。     

基于范畴论的本体描述方法

针对各种本体语言在描述本体过程中容易产生理解不一致的问题,利用范畴论的抽象性及图形化表示的优势,提出一种基于范畴论的本体描述方法,并给出了本体、本体映射和本体实例化的范畴论定义,其中本体被描述成范畴中的对象,本体间的映射被描述成范畴中对象间的同态射,本体实例化被描述成范畴间的函子。在此基础上,结合共极限和推出给出本体合并的描述及解释,并证明了本体合并的一些典型性质。