Ontology based text indexing and querying for the semantic web

This publication shows how the gap between the HTML based internet and the RDF based vision of the semantic web might be bridged, by linking words in texts to concepts of ontologies. Most current search engines use indexes that are built at the syntactical level and return hits based on simple string comparisons. However, the indexes do not contain synonyms, cannot differentiate between homonyms (‘mouse’ as a pointing vs. ‘mouse’ as an animal) and users receive different search results when they use different conjugation forms of the same word. In this publication, we present a system that uses ontologies and Natural Language Processing techniques to index texts, and thus supports word sense disambiguation and the retrieval of texts that contain equivalent words, by indexing them to concepts of ontologies.

For this purpose, we developed fully automated methods for mapping equivalent concepts of imported RDF ontologies (for this prototype WordNet, SUMO and OpenCyc). These methods will thus allow the seamless integration of domain specific ontologies for concept based information retrieval in different domains.

To demonstrate the practical workability of this approach, a set of web pages that contain synonyms and homonyms were indexed and can be queried via a search engine like query frontend. However, the ontology based indexing approach can also be used for other data mining applications such text clustering, relation mining and for searching free text fields in biological databases. The ontology alignment methods and some of the text mining principles described in this publication are now incorporated into the ONDEX system http://ondex.sourceforge.net/.     

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.     

电子商务环境下产品本体构建技术研究

产品本体通过构建产品类层次及其属性描述为交易双方提供了对产品共享的通用的理解。针对目前电子商务中标准产品本体缺乏产品属性描述的问题，根据电子商务网站中产品信息多以表格形式组织和描述的特点，提出以联合国标准产品与服务分类代码（UNSPSC）为核心本体，结合表格处理技术的半自动产品本体构建方法。以Web表格为对象，对Web表格的识别、表格规范化、单元产品本体及全局产品本体建立进行了研究。这种半自动的本体建立方法可以解决电子商务中的产品信息模型因缺乏标准化的属性描述而产生不一致性，实现对核心产品本体的扩展和补充。     

Ontologies for agents

An ontology is a computational model of some portion of the world. It is often captured in some form of a semantic network-a graph whose nodes are concepts or individual objects and whose arcs represent relationships or associations among the concepts. This network is augmented by properties and attributes, constraints, functions, and rules that govern the behavior of the concepts. Formally, an ontology is an agreement about a shared conceptualization, which includes frameworks for modeling domain knowledge and agreements about the representation of particular domain theories. Definitions associate the names of entities in a universe of discourse (for example, 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 names. For information systems, or for the Internet, ontologies can be used to organize keywords and database concepts by capturing the semantic relationships among the keywords or among the tables and fields in a database. The semantic relationships give users an abstract view of an information space for their domain of interest     

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.     

Towards a Machine of a Process (MOP) ontology to facilitate e-commerce of industrial machinery

Adapting to user's requirements is a key factor for enterprise success. Despite the existence of several approaches that point in this direction, simplifying integration and interoperability among users, suppliers and the enterprise during product lifecycle, is still an open issue. Ontologies have been used in some manufacturing applications and they promise to be a valid approach to model manufacturing resources of enterprises (e.g. machinery and raw material). Nevertheless, in this domain, most of the ontologies have been developed following methodologies based on development from scratch, thus ontologies previously developed have been discarded. Such ontological methodologies tend to hold the interoperability issues in some level. In this paper, a method that integrates ontology reuse with ontology validation and learning is presented. An upper (top-level) ontology for manufacturing was used as a reference to evaluate and to improve specific domain ontology. The evaluation procedure was based on the systemic methodology for ontology learning (SMOL). As a result of the application of SMOL, an ontology entitled Machine of a Process (MOP) was developed. The terminology included in MOP was validated by means of a text mining procedure called Term Frequency–Inverse Document Frequency (TF–IDF) which was carried out on documents from the domain in this study. Competency questions were performed on preexisting domain ontologies and MOP, proving that this new ontology has a performance better than the domain ontologies used as seed.     

Image retrieval with a multi-modality ontology

Ontologies represent domain concepts and relations in a form of semantic network. Many research works use ontologies in the information matchmaking and retrieval. This trend is further accelerated by the convergence of various information sources supported by ontologies. In this paper, we propose a novel multi-modality ontology model that integrates both the low-level image features and the high-level text information to represent image contents for image retrieval. By embedding this ontology into an image retrieval system, we are able to realize intelligent image retrieval with high precision. Moreover, benefiting from the soft-coded ontology model, this system has good flexibility and can be easily extended to the larger domains. Currently, our experiment is conducted on the animal domain canine. An ontology has been built based on the low-level features and the domain knowledge of canine. A prototype retrieval system is set up to assess the performance. We compare our experiment results with traditional text-based image search engine and prove the advantages of our approach.     

A visual tool for ontology alignment to enable geospatial interoperability

In distributed geospatial applications with heterogeneous databases, an ontology-driven approach to data integration relies on the alignment of the concepts of a global ontology that describe the domain, with the concepts of the ontologies that describe the data in the distributed databases. Once the alignment between the global ontology and each distributed ontology is established, agreements that encode a variety of mappings between concepts are derived. In this way, users can potentially query hundreds of geospatial databases using a single query. Using our approach, querying can be easily extended to new data sources and, therefore, to new regions. In this paper, we describe the AgreementMaker, a tool that displays the ontologies, supports several mapping layers visually, presents automatically generated mappings, and finally produces the agreements.     

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.     

DeMO: An Ontology for Discrete-event Modeling and Simulation

Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community.     

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.     

Reflections on a medical ontology

In this paper we confront the divide between the ontologies developed from the requirement of comprehensive and general domain coverage and those devised to meet application-specific requirements. While the generalists typically attach philosophical sophistication to their approach, in supposed contrast to the narrow remit chosen by the application-bound knowledge engineers, we would like to indicate that the latter practice can often reflect a multi-faceted rationale, nuanced by the requirements of the domain.We demonstrate how the necessity of placing ontology-based systems with the work-practices of domain experts introduces unique demands on design rationales and enforces, often implicitly, a philosophical assessment of the necessary concepts and relations that balance the generality and specificity. Such demands are not addressed by generic approaches to modelling the reality of a domain. Indeed, we articulate the philosophical and practical considerations that we have taken into account when developing an application-specific ontology. We would certainly hope that our experiences can be of help to the development of ontologies in similar applications.     

OntoPlus: Text-driven ontology extension using ontology content,structure and co-occurrence information

This paper addresses the process of semi-automatic text-driven ontology extension using ontology content, structure and co-occurrence information. A novel OntoPlus methodology is proposed for semi-automatic ontology extension based on text mining methods. It allows for the effective extension of the large ontologies, providing a ranked list of potentially relevant concepts and relationships given a new concept (e.g., glossary term) to be inserted in the ontology. A number of experiments are conducted, evaluating measures for ranking correspondence between existing ontology concepts and new domain concepts suggested for the ontology extension. Measures for ranking are based on incorporating ontology content, structure and co-occurrence information. The experiments are performed using a well known Cyc ontology and textual material from two domains – finances and, fisheries & aquaculture. Our experiments show that the best results are achieved by combining content, structure and co-occurrence information. Furthermore, ontology content and structure seem to be more important than co-occurrence for our data in the financial domain. At the same time, ontology content and co-occurrence seem to have higher importance for our fisheries & aquaculture domain.     

Supporting the discovery and labeling of non-taxonomic relationships in ontology learning

Ontology learning (OL) from texts has been suggested as a technology that helps to reduce the bottleneck of knowledge acquisition in the construction of domain ontologies. In this learning process, the discovery, and possibly also labeling, of non-taxonomic relationships has been identified as one of the most difficult and often neglected problems. In this paper, we propose a technique that addresses this issue by analyzing a domain text corpus to extract verbs frequently applied for linking certain pairs of concepts. Integrated in an ontology building process, this technique aims to reduce the work-load of knowledge engineers and domain experts by suggesting candidate relationships that might become part of the ontology as well as prospective labels for them.     

Where to publish and find ontologies? A survey of ontology libraries

One of the key promises of the Semantic Web is its potential to enable and facilitate data interoperability. The ability of data providers and application developers to share and reuse ontologies is a critical component of this data interoperability: if different applications and data sources use the same set of well defined terms for describing their domain and data, it will be much easier for them to “talk” to one another. Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies. Thus ontology libraries can serve as a link in enabling diverse users and applications to discover, evaluate, use, and publish ontologies. In this paper, we provide a survey of the growing—and surprisingly diverse—landscape of ontology libraries. We highlight how the varying scope and intended use of the libraries affects their features, content, and potential exploitation in applications. From reviewing 11 ontology libraries, we identify a core set of questions that ontology practitioners and users should consider in choosing an ontology library for finding ontologies or publishing their own. We also discuss the research challenges that emerge from this survey, for the developers of ontology libraries to address.     

Evaluating ontologies: Towards a cognitive measure of quality

Ontologies are formal specifications of shared conceptualizations of a domain. Important applications of ontologies include distributed knowledge-based systems, such as the semantic web, and the evaluation of modelling languages, e.g. for business process or conceptual modelling. These applications require formal ontologies of good quality. The quality of a formal ontology requires both a good conceptualization of a domain and a good specification of the conceptualization. In this paper, we focus on the latter aspect, and present a method to test how well a specification of a formal ontology corresponds to a conceptualization of a domain held by ontology users. Our experimental method is based on principles of cognitive psychology. We present two experiments to demonstrate our method using upper-level ontologies.     

Identifying relevant concept attributes to support mapping maintenance under ontology evolution

The success of distributed and semantic-enabled systems relies on the use of up-to-date ontologies and mappings between them. However, the size, quantity and dynamics of existing ontologies demand a huge maintenance effort pushing towards the development of automatic tools supporting this laborious task. This article proposes a novel method, investigating different types of similarity measures, to identify concepts’ attributes that served to define existing mappings. The obtained experimental results reveal that our proposed method allows to identify the relevant attributes for supporting mapping maintenance, since we found correlations between ontology changes affecting the identified attributes and mapping changes.     

A methodology for constructing of philosophy ontology based on philosophical texts

An ontology is a crucial factor for the success of the Semantic Web and other knowledge-based systems in terms of share and reuse of domain knowledge. However, there are a few concrete ontologies within actual knowledge domains including learning domains. In this paper, we develop an ontology which is an explicit formal specification of concepts and semantic relations among them in philosophy. We call it a philosophy ontology. Our philosophy is a formal specification of philosophical knowledge including knowledge of contents of classical texts of philosophy. We propose a methodology, which consists of detailed guidelines and templates, for constructing text-based ontology. Our methodology consists of 3 major steps and 14 minor steps. To implement the philosophy ontology, we develop an ontology management system based on Topic Maps. Our system includes a semi-automatic translator for creating Topic Map documents from the output of conceptualization steps and other tools to construct, store, retrieve ontologies based on Topic Maps. Our methodology and tools can be applied to other learning domain ontologies, such as history, literature, arts, and music.     

An approach for sub-ontology evolution in a distributed health care enterprise

In response to the changing nature of health issues, standardized health ontologies such as SNOMED CT and UMLS incline to change more frequently than most other domain ontologies. Yet, semantic interoperability shared among institutions within a distributed health care enterprise relies heavily on the availability of a valid and up-to-date standardized ontology. In this paper, we propose the creation and preservation of sub-ontologies to deal with the frequent changes in health ontologies. Our approach focuses on the nature and characteristics of standard health ontologies, however it can also be applied to other domain ontologies with similar characteristics. Our sub-ontology evolution approach defines ways to create valid sub-ontologies for each specific health application, and to effectively develop a series of propagation mechanism when the main ontology changes. Our approach will (i) isolate the required change propagation to the relevant health applications that utilized the changing concepts only, and (ii) optimize the propagation mechanism to include the minimum number of operations only. Since a sub-ontology should be a valid ontology by itself, the change propagation approach used in this process should contain the rules to assure the validity of the produced sub-ontology while keeping the consistency of the sub-ontology to the evolved base ontology. A change identification process, which considers the nature of the health ontology change logs, is conducted to identify the semantics of the changes. From the evaluation, it is shown that the content of the evolved sub-ontologies produced using our approach is consistent to the evolved base ontology. Moreover, the propagation process can be performed more efficiently because the number of operations required for our change propagation method is lower than the number of operations required for direct re-extraction from the evolved base ontology.