Survey of modular ontology techniques and their applications in the biomedical domain

In the past several years, various ontologies and terminologies such as the Gene Ontology have been developed to enable interoperability across multiple diverse medical information systems. They provide a standard way of representing terms and concepts thereby supporting easy transmission and interpretation of data for various applications. However, with their growing utilization, not only has the number of available ontologies increased considerably, but they are also becoming larger and more complex to manage. Toward this end, a growing body of work is emerging in the area of modular ontologies where the emphasis is on either extracting and managing "modules" of an ontology relevant to a particular application scenario (ontology decomposition) or developing them independently and integrating into a larger ontology (ontology composition). In this paper, we investigate state-of-the-art approaches in modular ontologies focusing on techniques that are based on rigorous logical formalisms as well as well-studied graph theories. We analyze and compare how such approaches can be leveraged in developing tools and applications in the biomedical domain. We conclude by highlighting some of the limitations of the modular ontology formalisms and put forward additional requirements to steer their future development.     

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.     

ANEMONE: An environment for modular ontology development

Many real-world ontologies contain thousands of terms and are developed by multiple participants. The use of monolithic ontologies can cause problems that affect various stages of the ontology life cycle. Thus, there is an urgent need for tools and methodologies that facilitate modular ontology design. The benefits of a modular approach include division of labor, scalability, partial reuse, and broadened participation. This article presents a methodology for modular ontology development. The main idea is to facilitate an interoperable hierarchical network of ontology modules. Modules are designed as a combination of more abstract modules in higher levels of the hierarchy. This methodology differs from previous methodologies in the way that it defines concrete development steps, to facilitate use by both naive and expert ontology developers. This methodology is also supported by ontology design patterns and a prototypical ontology development tool.     

A comprehensive framework for the evaluation of ontology modularization

The Semantic Web and ontologies have received increased attention in recent years. The delivery of well-designed ontologies enhances the effect of Semantic Web services, but building ontologies from scratch requires considerable time and effort. Modularizing ontologies and integrating ontology modules to a given context help users effectively develop ontologies and revitalize ontology dissemination. Therefore, various tools for modularizing ontologies have been developed. However, selecting an appropriate tool to fit a given context is difficult because the assumptions for the approaches greatly vary. Therefore, a suitable framework is required to compare and help screen the most suitable modularization tool.In this research, we propose a new evaluation framework for selecting an appropriate ontology modularization tool. We present three aspects of tool evaluation as the main dimensions for the assessment of modularization tools: tool performance, data performance, and usability.This study provides an implicit evaluation and an empirical analysis of three modularization tools. It also provides an evaluation method for ontology modularization, enabling ontology engineers to compare different modularization tools and easily choose an appropriate one for the production of qualifying ontology modules.The experimental results indicate that the proposed evaluation criteria for ontology modularization tools are valid and effective. This research provides a useful method for assessing and selecting ontology modularization tools. Modularization performance, data performance, and usability are the three modularization aspects designed and applied to the context of ontology. We provide a new focus on the comprehensive framework to evaluate the performance and usability of ontology modularization tools. The proposed framework should be of value to both ontology engineers, who are interested in ontology modularization, and to practitioners, who need information on how to evaluate and select a specific type of ontology tool in accordance with the requirements of the individual environment.     

基于本体模块接口的入侵防御系统研究

建立一种新型分布式入侵防御模型并进行应用示例,该模型的知识库采用基于接口的模块化本体,防御方法采用上下文相关的策略。模块化本体能有效克服单一本体推理效率低、扩展性差等缺点,而在模块化本体中采用接口的方法有利于模块的独立进化和灵活配置。本体模块通过发送事件消息能够高效、及时地进行知识更新。     

本体模块化的研究与实现

将软件工程中模块化的思想引入本体知识库的构建过程中,将本体组织成多个本体模块的集成形式,这样不仅方便了本体的构建,更有利于本体知识库的共享、重用和维护.用模块化的方法构建了汽车驾驶培训领域本体,建立方法库,在本体模块间用查询方式实现模块间的通信.这样的开发经验可以推广到其他领域.     

基于本体映射的多本体查询方法

随着语义网的发展,本体已经成为很多领域表达知识的主要手段。许多领域都根据自己的需求建立了本体来描述本领域内的知识。但是目前许多针对本体的语义查询只能对一个本体进行查询。为了实现一个查询能够对多个本体进行访问并且返回适当的查询结果,文中提出了一种利用本体映射实现对多本体的查询方法。其中的映射方法是一种基于语义的多策略结合方式。通过实验发现查询的速度与本体的数量基本呈线性关系且不会因为本体异构程度而增加。     

Using JessTab to integrate Protege and Jess

Integration with external systems, such as problem solvers, is becoming increasingly important for ontology development and knowledge-modeling tools. The author's JessTab extension lets you write Jess programs that manage Protege ontologies and knowledge bases. Protege is a popular, modular ontology development and knowledge acquisition tool.     

A multi-strategy knowledge interoperability framework for heterogeneous learning objects

This paper presents a knowledge exchange framework that can leverage the interoperability among semantically heterogeneous learning objects. With the release of various e-Learning standards, learning contents and digital courses are easy to achieve cross-platform sharing, exchanging, and even reorganizing. However, knowledge sharing in semantic level is still a challenge due to that the learning materials can be presented in any form, such as audios, videos, web pages, and even flash files. The proposed knowledge exchange framework allows users to share their learning materials (also called “learning objects”) in semantic level automatically. This framework contains two methodologies: the first is a semantic mapping between knowledge bases (i.e. ontologies) which have essentially similar concepts, and the second is an ontology-based classification algorithm for sharable learning objects. The proposed algorithm adopts the IMS DRI standard and classifies the sharable learning objects from heterogeneous repositories into a local knowledge base by their inner meaning instead of keyword matching. Significance of this research lies in the semantic inferring rules for ontology mapping and learning objects classification as well as the full automatic processing and self-optimizing capability. Focused on digital learning materials and contrasted to other traditional technologies, the proposed approach has experimentally demonstrated significantly improvement in performance.     

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.     

A semantical framework for hybrid knowledge bases

In the ongoing discussion about combining rules and ontologies on the Semantic Web a recurring issue is how to combine first-order classical logic with nonmonotonic rule languages. Whereas several modular approaches to define a combined semantics for such hybrid knowledge bases focus mainly on decidability issues, we tackle the matter from a more general point of view. In this paper, we show how Quantified Equilibrium Logic (QEL) can function as a unified framework which embraces classical logic as well as disjunctive logic programs under the (open) answer set semantics. In the proposed variant of QEL, we relax the unique names assumption, which was present in earlier versions of QEL. Moreover, we show that this framework elegantly captures the existing modular approaches for hybrid knowledge bases in a unified way.     

Agent-based ontology mapping and integration towards interoperability

Abstract: Interoperability is an important issue in ontology research. In this paper, a novel agent-based framework for managing ontologies in a dynamic environment is developed. The framework has several key characteristics such as flexibility and extensibility that differentiate this research from others. Based on the proposed framework, ontology mapping and integration are investigated. It is believed that inter-ontology processes like ontology mapping with logical semantics are foundations of ontology-based applications. Accordingly, several types of semantic relations are proposed and corresponding mapping mechanisms are developed. Based on mapping results, ontology integration is developed to provide abstract views for participating organizations in the presence of a variety of ontologies. A prototype is built to demonstrate the design and functionalities and is applied to beer ontologies. The prototype shows that the framework is not only flexible but also practical. All agents derived from the framework exhibit their behaviours as expected.     

Analyzing a firm’s international portfolio of technological knowledge: A declarative ontology-based OWL approach for patent documents

Patent databases contain large amounts of information about the inventions and metadata of corporate patents (such as the technological domain they belong to, their applicants, and inventors). These databases are available online but since they do not provide explicit information about the relationships between different patent metadata, it is not possible for computers to automatically process such relationships. Several patent ontologies have been proposed so far in order to provide patent knowledge bases with semantics by merging information from different databases and establishing a common vocabulary. However, previous ontology literature has paid limited attention to the representation of specific relationships among metadata and the design of reasoning procedures that would allow some information not explicitly specified in the databases or ontologies to be inferred. This article proposes a methodological approach for the definition of relationships and reasoning tasks for patent analysis by using patent ontologies, and provides a real illustration of its potential in the context of international flows of research knowledge. This declarative method is based on the formal definition of key patent analysis indicators (KPAIs). The case study analysis is relevant because global competition and the importance of multinational firms in the patent process have resulted in firms not only patenting on their domestic markets but also transferring their patents to other markets and developing patents in different countries. In this context, it is important to analyze the connections between the patenting processes and the international knowledge flows of research and development. More specifically, the paper illustrates the applicability of the proposed methodology by classifying patents into the five patterns of internationalization identified by the Organization for Economic Co-operation and Development (OECD).     

Developing a modular hydrogeology ontology by extending the SWEET upper-level ontologies

Upper-level ontologies comprise general concepts and properties which need to be extended to include more diverse and specific domain vocabularies. We present the extension of NASA's Semantic Web for Earth and Environmental Terminology (SWEET) ontologies to include part of the hydrogeology domain. We describe a methodology that can be followed by other allied domain experts who intend to adopt the SWEET ontologies in their own discipline. We have maintained the modular design of the SWEET ontologies for maximum extensibility and reusability of our ontology in other fields, to ensure inter-disciplinary knowledge reuse, management, and discovery.The extension of the SWEET ontologies involved identification of the general SWEET concepts (classes) to serve as the super-class of the domain concepts. This was followed by establishing the special inter-relationships between domain concepts (e.g., equivalence for vadose zone and unsaturated zone), and identifying the dependent concepts such as physical properties and units, and their relationship to external concepts. Ontology editing tools such as SWOOP and Protégé were used to analyze and visualize the structure of the existing OWL files. Domain concepts were introduced either as standalone new classes or as subclasses of existing SWEET ontologies. This involved changing the relationships (properties) and/or adding new relationships based on domain theories. In places, in the Owl files, the entire structure of the existing concepts needed to be changed to represent the domain concept more meaningfully. Throughout this process, the orthogonal structure of SWEET ontologies was maintained and the consistency of the concepts was tested using the Racer reasoner. Individuals were added to the new concepts to test the modified ontologies. Our work shows that SWEET ontologies can successfully be extended and reused in any field without losing their modular or reference structure, or disrupting their URI links.     

Thesaurus or Logical Ontology,Which One Do We Need for Text Mining?

Ontologies are recognised as important tools, not only for effective and efficient information sharing, but also for information extraction and text mining. In the biomedical domain, the need for a common ontology for information sharing has long been recognised, and several ontologies are now widely used. However, there is confusion among researchers concerning the type of ontology that is needed for text mining , and how it can be used for effective knowledge management, sharing, and integration in biomedicine. We argue that there are several different ways to define an ontology and that, while the logical view is popular for some applications, it may be neither possible nor necessary for text mining. We propose a text-centered approach for knowledge sharing, as an alternative to formal ontologies. We argue that a thesaurus (i.e. an organised collection of terms enriched with relations) is more useful for text mining applications than formal 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.     

Cohesion and coupling metrics for ontology modules

In recent years, an increasing number of ontologies and semantic web applications have been developed and used. A conscious effort has been made to develop methods to modularize ontologies. These methods contribute to building a new ontology. However, few studies have focused on the evaluative methods for ontology modules. In this study, we propose novel metrics to measure ontology modularity. To evaluate the ontology modules, we introduce cohesion and coupling based on the theory of software metrics. A cohesion metric and two coupling metrics were used to measure cohesion and coupling for ontology modules. The proposed metrics provide more detailed support in considering the different types of relationships between classes in ontology modules. In addition, the new coupling metrics contribute to checking the consistency between the ontology modules and their original ontology. The proposed metrics were validated using well-known verification frameworks and empirical experiments to complement the previous investigations. The results of this study offer ontology engineers valuable criteria with which to evaluate ontology modules and help ontology users select qualifying ontology modules.