Semantic similarity estimation from multiple ontologies

The estimation of semantic similarity between words is an important task in many language related applications. In the past, several approaches to assess similarity by evaluating the knowledge modelled in an ontology have been proposed. However, in many domains, knowledge is dispersed through several partial and/or overlapping ontologies. Because most previous works on semantic similarity only support a unique input ontology, we propose a method to enable similarity estimation across multiple ontologies. Our method identifies different cases according to which ontology/ies input terms belong. We propose several heuristics to deal with each case, aiming to solve missing values, when partial knowledge is available, and to capture the strongest semantic evidence that results in the most accurate similarity assessment, when dealing with overlapping knowledge. We evaluate and compare our method using several general purpose and biomedical benchmarks of word pairs whose similarity has been assessed by human experts, and several general purpose (WordNet) and biomedical ontologies (SNOMED CT and MeSH). Results show that our method is able to improve the accuracy of similarity estimation in comparison to single ontology approaches and against state of the art related works in multi-ontology similarity assessment.     

Determining semantic similarity among entity classes from different ontologies

Semantic similarity measures play an important role in information retrieval and information integration. Traditional approaches to modeling semantic similarity compute the semantic distance between definitions within a single ontology. This single ontology is either a domain-independent ontology or the result of the integration of existing ontologies. We present an approach to computing semantic similarity that relaxes the requirement of a single ontology and accounts for differences in the levels of explicitness and formalization of the different ontology specifications. A similarity function determines similar entity classes by using a matching process over synonym sets, semantic neighborhoods, and distinguishing features that are classified into parts, functions, and attributes. Experimental results with different ontologies indicate that the model gives good results when ontologies have complete and detailed representations of entity classes. While the combination of word matching and semantic neighborhood matching is adequate for detecting equivalent entity classes, feature matching allows us to discriminate among similar, but not necessarily equivalent entity classes.     

Joint semantic similarity assessment with raw corpus and structured ontology for semantic-oriented service discovery

Semantic-oriented service matching is one of the challenges in automatic Web service discovery. Service users may search for Web services using keywords and receive the matching services in terms of their functional profiles. A number of approaches to computing the semantic similarity between words have been developed to enhance the precision of matchmaking, which can be classified into ontology-based and corpus-based approaches. The ontology-based approaches commonly use the differentiated concept information provided by a large ontology for measuring lexical similarity with word sense disambiguation. Nevertheless, most of the ontologies are domain-special and limited to lexical coverage, which have a limited applicability. On the other hand, corpus-based approaches rely on the distributional statistics of context to represent per word as a vector and measure the distance of word vectors. However, the polysemous problem may lead to a low computational accuracy. In this paper, in order to augment the semantic information content in word vectors, we propose a multiple semantic fusion (MSF) model to generate sense-specific vector per word. In this model, various semantic properties of the general-purpose ontology WordNet are integrated to fine-tune the distributed word representations learned from corpus, in terms of vector combination strategies. The retrofitted word vectors are modeled as semantic vectors for estimating semantic similarity. The MSF model-based similarity measure is validated against other similarity measures on multiple benchmark datasets. Experimental results of word similarity evaluation indicate that our computational method can obtain higher correlation coefficient with human judgment in most cases. Moreover, the proposed similarity measure is demonstrated to improve the performance of Web service matchmaking based on a single semantic resource. Accordingly, our findings provide a new method and perspective to understand and represent lexical semantics.     

本体相似度研究

不同本体之间的交互成为语义Web的首要任务,其中本体相似度计算是本体映射的关健环节。在以往的研究中,本体相似度计算通常专注于模式及其结构的匹配。目前研究朝着进一步考虑本体内部语义信息方向努力。本文描述了语义相似度栈的各个层次,依据各个层次的语义特征对目前本体相似度方法进行分类,并对每种方法进行了详细描述。最后对现有一些主要的本体间相似度计算方法进行归纳总结。这项研究工作将为人们提出新的相似度方法或者组合的计算方法作一个参考。     

MD4：一种综合的跨本体实体语义相似度计算方法*

面向广域分布环境下信息资源共享与服务的需要,设计了基于本体的元数据模型,并在MD3模型的基础上给出了一种基于该元数据模型的跨本体的语义相似度计算方法——MD4模型。MD4充分利用本体对实体的描述信息,重点讨论了实体名称、实体属性、实体语义环境以及实体实例等相似度的计算,把MD3模型扩展到MD4模型,使得信息资源实体间语义相似度的计算更全面、精确。     

语义集成:本体映射方法研究

本体是客观世界知识的表现形式,随着语义Web研究的深入,研究者们构建了越来越多的本体,如何实现本体之间的知识共享和重用,成为了语义Web发展的关键。文中对本体映射的方法进行了研究,系统阐述了本体及本体映射的定义、本体映射中的相似度计算和本体映射框架等。如何减少本体映射中的人工干预,实现本体的半自动化或自动化映射将是该领域的发展方向。     

Ontology selection ranking model for knowledge reuse

Ontology reuse is recommended as a key factor to develop cost-effective and high-quality ontologies because it could reduce development costs by avoiding rebuilding existing ontologies. Selecting the desired ontology from existing ontologies is essential for ontology reuse. Until now, much research on ontology selection has focused on lexical-level support. However, in these cases, it is almost impossible to find an ontology that includes all the concepts matched by the search terms at the semantic level. Finding an ontology that meets users’ needs requires a new ontology selection and ranking mechanism based on semantic similarity matching. We propose an ontology selection and ranking model consisting of selection standards and metrics based on better semantic matching capabilities. The model we propose presents two novel features different from previous research models. First, it enhances the ontology selection and ranking method practically and effectively by enabling semantic matching of taxonomy or relational linkage between concepts. Second, it identifies what measures should be used to rank ontologies in the given context and what weight should be assigned to each selection measure.     

面向模块重用的描述逻辑SHJF本地性规则研究

可重用本体模块的抽取是本体重用的一个关键环节。与传统工程应用中使用的基于本体层次的结构化方法抽取本体模块相比,使用逻辑的方法能充分利用本体提供的语义信息,抽取的本体模块更具完整性和正确性。在研究保守扩展的本体模块理论基础上,根据Grau B C提出的 SHOJQ 本地性规则,提出并证明了描述逻辑SHJF对应的语义本地性规则和句法本地性规则,为基于该规则抽取可重用本体模块提供了理论基础。     

Variable weight semantic graph‐based ontology mapping method

The mapping method that is based on the name and structure of the ontology elements is the strategy used in most mapping methods. Methods using the name often only use the similarity between the individual elements in the ontology to predict the semantic relations between two ontologies, while the latter measure the mapping between two ontologies by means of the structural relations between the elements. The effects of these two kinds of mapping strategies are not ideal. Addressing this issue, the work presented in this paper proposes an ontology mapping approach, in which the ontology element name and structure are combined. It uses the approaches based on linguistics and distance to generate a variable weight semantic graph. On this graph, the similarity of element names and structure are calculated through iterative computation. In the process of iteration, similarity result values are constantly adjusted. The approach avoids the problem of single methods that cannot use the entire amount of ontology information; therefore, it provides a more ideal mapping result. For making full use of the message of ontology, our implementation and experimental results are provided to demonstrate the effectiveness of the mapping approach.     

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。     

基于本体集成的语义标注模型设计

语义Web的全面实现需借助于语义标注,标注网页信息会涉及到多个本体.据此,通过研究桥本体,提出一个在本体集成的基础上建立起来的多本体语义标注模型.该模型利用桥本体集成顶层本体和多个领域本体,同时借助基于本体的信息抽取技术对网页进行语义标注,并将标注信息存入标注库,使标注信息与网页分离,提高语义检索的效率.通过举例说明了本模型的合理性.     

Axiom-based ontology matching

Abstract: Managing multiple ontologies is now a core question in most of the applications that require semantic interoperability. The semantic web is surely the most significant application of this report: the current challenge is not to design, develop and deploy domain ontologies but to define semantic correspondences among multiple ontologies covering overlapping domains. In this paper, we introduce a new approach of ontology matching named axiom-based ontology matching. As this approach is founded on the use of axioms, it is mainly dedicated to heavyweight ontologies, but it can also be applied to lightweight ontologies as a complementary approach to the current techniques based on the analysis of natural language expressions, instances and/or taxonomical structures of ontologies. This new matching paradigm is defined in the context of the conceptual graphs model, where the projection (i.e. the main operator for reasoning with conceptual graphs which corresponds to homomorphism of graphs) is used as a means to semantically match the concepts and the relations of two ontologies through the explicit representation of the axioms in terms of conceptual graphs. We also introduce an ontology of representation, called MetaOCGL, dedicated to the reasoning of heavyweight ontologies at the meta-level.     

Resolution of Semantic Heterogeneity in Database Schema Integration Using Formal Ontologies

This paper addresses the problem of handling semantic heterogeneity during database schema integration. We focus on the semantics of terms used as identifiers in schema definitions. Our solution does not rely on the names of the schema elements or the structure of the schemas. Instead, we utilize formal ontologies consisting of intensional definitions of terms represented in a logical language. The approach is based on similarity relations between intensional definitions in different ontologies. We present the definitions of similarity relations based on intensional definitions in formal ontologies. The extensional consequences of intensional relations are addressed. The paper shows how similarity relations are discovered by a reasoning system using a higher-level ontology. These similarity relations are then used to derive an integrated schema in two steps. First, we show how to use similarity relations to generate the class hierarchy of the global schema. Second, we explain how to enhance the class definitions with attributes. This approach reduces the cost of generating or re-generating global schemas for tightly-coupled federated databases.     

SVM-based ontology matching approach

There are a lot of heterogeneous ontologies in semantic web, and the task of ontology mapping is to find their semantic relationship. There are integrated methods that only simply combine the similarity values which are used in current multi-strategy ontology mapping. The semantic information is not included in them and a lot of manual intervention is also needed, so it leads to that some factual mapping relations are missed. Addressing this issue, the work presented in this paper puts forward an ontology matching approach, which uses multi-strategy mapping technique to carry on similarity iterative computation and explores both linguistic and structural similarity. Our approach takes different similarities into one whole, as a similarity cube. By cutting operation, similarity vectors are obtained, which form the similarity space, and by this way, mapping discovery can be converted into binary classification. Support vector machine (SVM) has good generalization ability and can obtain best compromise between complexity of model and learning capability when solving small samples and the nonlinear problem. Because of the said reason, we employ SVM in our approach. For making full use of the information of ontology, our implementation and experimental results used a common dataset to demonstrate the effectiveness of the mapping approach. It ensures the recall ration while improving the quality of mapping results.     

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.     

Semantic Similarity between Ontologies at Different Scales

In the past decade, existing and new knowledge and datasets have been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three gene ontology slims (plant, yeast, and candida, among which the latter two belong to the same kingdom - fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performances of Jiang- Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by 1) consistently showing that yeast and candida are more similar (as compared to plant) at different scales, and 2) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.      

基于本体相似度的中文科研论文信息抽取

随着大量的科研论文出现在互联网上,从中精确地抽取论文头部信息和引文信息显得十分重要。提出了基于本体相似度的信息抽取方法,该方法的关键在于用本体相似度判定某个行本体是正例还是反例,然后通过主动学习选择最有可能包含抽取信息的行本体集,再充分利用本体的语义推理能力找到正确的片断。从论文中提取头部信息和引文信息为进一步的语义检索和语义存储奠定基础。测试数据集的实验结果显示该方法比其他方法具有较高的准确率。     

一种跨本体的语义相似度计算方法

针对在广域分布环境下进行信息共享与服务的需要,本文设计了基于本体的元数据模型,并在MD3模型的基础上给出了一种基于该元数据模型的跨本体的语义相似度计算方法.MD3模型是一种系统的跨本体概念间相似度的计算方法,这种方法无需建立一个集成的共享本体.在MD3模型的基础上,充分利用本体对概念的描述信息,重点讨论了跨本体概念间非层次关系相似度的计算,把MD3模型扩展到MD4模型,使得概念间相似度的计算理论上更全面、更精确.     

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.