• Title/Summary/Keyword: ontology

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Integrative Analysis of Microarray Data with Gene Ontology to Select Perturbed Molecular Functions using Gene Ontology Functional Code

  • Kim, Chang-Sik;Choi, Ji-Won;Yoon, Suk-Joon
    • Genomics & Informatics
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    • v.7 no.2
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    • pp.122-130
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    • 2009
  • A systems biology approach for the identification of perturbed molecular functions is required to understand the complex progressive disease such as breast cancer. In this study, we analyze the microarray data with Gene Ontology terms of molecular functions to select perturbed molecular functional modules in breast cancer tissues based on the definition of Gene ontology Functional Code. The Gene Ontology is three structured vocabularies describing genes and its products in terms of their associated biological processes, cellular components and molecular functions. The Gene Ontology is hierarchically classified as a directed acyclic graph. However, it is difficult to visualize Gene Ontology as a directed tree since a Gene Ontology term may have more than one parent by providing multiple paths from the root. Therefore, we applied the definition of Gene Ontology codes by defining one or more GO code(s) to each GO term to visualize the hierarchical classification of GO terms as a network. The selected molecular functions could be considered as perturbed molecular functional modules that putatively contributes to the progression of disease. We evaluated the method by analyzing microarray dataset of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Based on the integration approach, we selected several interesting perturbed molecular functions that are implicated in the progression of breast cancers. Moreover, these selected molecular functions include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting perturbed molecular functions that putatively play roles in the progression of diseases and provides an improved interpretability of GO terms based on the definition of Gene Ontology codes.

The ontology development for broadcast content metadata (방송 콘텐츠 메타데이터를 위한 온톨로지 개발)

  • Ham, Jong-Wan;Baek, Seung-Il;Kim, Nam-Hoon;Jung, Hoe-Kyung
    • Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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    • pp.591-593
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    • 2010
  • The Ontology is the concept of human beings in any sense to classify things as departure from the classification based on the meaning at the prensent situation and concepts as the object of the Ontology. also, the technology is shared the conceptualization in a formal ontology as a meaning to give a clear description to the conceptual engineering in the ontology. Specialized multimedia broadcasting of TV-Anytime standard and multimedia representation of the overall standard of the MPEG-7 based on the concept of broadcasting multimedia presentations that can be used to develop an ontology who is required. In this paper, in TV-Anytime and MPEG-7 multimedia standard for broadcasting multimedia contents based on standards developed for the ontology, an ontology language for expressing OWL (Web Ontology Language) and RDF (Resource Description Framework) and the broadcast contents using To represent metadata of the system who has been developed.

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Development and Evaluation of Ontology for Diagnosis in Oriental Medicine (한의진단 Ontology 구축과 평가)

  • Shin Sang-Woo;Jung Gil-San;Park Kyung-Mo;Kim Seon-Ho;Park Jong-Hyun
    • Journal of Physiology & Pathology in Korean Medicine
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    • v.20 no.1
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    • pp.202-208
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    • 2006
  • The goal of this study is to develop knowledge representation method for the construction and evaluation of ontology for diagnosis in oriental medicine. To develop the expert system for decision making on diagnosis and treatment, the systematic and structural knowledge which can be processible in EMR(Electronic Medical Record) must be precedent, and the Computational Process which control the system as well. This study set up an ontology as a trial model to represent the oriental medical knowledge into the machine processible one. Protege 2.1 has been used to build the ontology, and the serialization format of our ontology is the XML document based on OWL. The components of oriental medical diagnosis was arranged with the combination of symptoms which belong to the certain symptom patterns. Then natural language which expresses the oriental medical diagnosis components were converted into the logical sentence, and individual characteristic symptoms into each values of specific properties. In addition to the study, the diagnosis software for oriental medicine was developed and it used the ontology which we developed. Sequently, we tested the software to confirm the appropriateness of ontology. The result of the test shows that diagnostic questions are automatically formulated according to the diagnosis components of this ontology and that as such diagnostic results are induced. Therefore, the ontology system in this study will be efficient to develop the diagnosis program and useful as a tool for doctors to make decision. But, it is not recommendable to apply the system to the clinical environment until the clear diagnosis standards are introduced, and the more reliable diagnosis program can be developed based on the more appropriate ontology mentioned above.

GO Guide : Browser & Query Translation for Biological Ontology (GO Guide : 생물학 온톨로지를 위한 브라우저 및 질의 변환)

  • Jung Jun-Won;Park Hyoung-Woo;Im Dong-Hhyuk;Lee Kang-Pyo;Kim Hyoung-Joo
    • Journal of KIISE:Computing Practices and Letters
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    • v.12 no.3
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    • pp.183-191
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    • 2006
  • As genetic research is getting more active, data construction of genes are needed in the field of biology. Therefore, Gene Ontology Consortium has constructed genetic information by OWL, which is Ontology description language published by W3C. However, previous browsers for Gene Ontology only support simple searching mechanisms based on keyword, tree, and graph, but it is not able to search high quality information considering various relationships. In this paper, we suggest browsing technique which integratesvarious searching methods to support researchers who are doing actually experiment in biology field. Also, instead of typing a query, we propose querv generation technique which constructs query while browsing and query translation technique which translate generated query into SeRQL query It is convenient for user and enables user to obtain high quality information. And by this GO Guide browser, it has been shown that the information of Gene Ontology could be used efficiently.

Matching Method between Heterogeneous Data for Semantic Search (시맨틱 검색을 위한 이기종 데이터간의 매칭방법)

  • Lee, Ki-Jung;WhangBo, Taeg-Keun
    • The Journal of the Korea Contents Association
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    • v.6 no.10
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    • pp.25-33
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    • 2006
  • For semantic retrieval in semantic web environment, it is an important factor to manage and manipulate distributed resources. Ontology is essential for efficient search in distributed resources, but it is almost impossible to construct an unified ontology for all distributed resources in the web. In this paper, we assumed that most information in the web environment exist in the form of RDBMS, and propose a matching method between domain ontology and the existing RDBMS tables for semantic retrieval. Most previous studies about matching between RDBMS tables and domain ontology have extracted a local ontology from RDBMS tables at first, and conducted the matching between the local ontology and domain ontology. However in the processing of extracting a local ontology, some problems such as losing domain information can be occurred since its correlation with domain ontology has not been considered at all. In this paper, we propose a methods to prevent the loss of domain information through the similarity measure between instances of RDBMS tables and instances of ontology. And using the relational information between RDBMS tables and the relational information between classes in domain ontology, more efficient instance-based matching becomes possible.

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Semantic Search based on Event Ontology (이벤트 온톨로지 기반의 의미 정보 검색)

  • Han, Yong-Jin;Park, Se-Young;Lee, Young-Hwa;Kim, Kweon-Yang
    • Journal of KIISE:Computing Practices and Letters
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    • v.14 no.1
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    • pp.96-100
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    • 2008
  • An ontology provides an explicit specification of concepts and relations on information extracted from database or on human knowledge. Using an ontology, The information can be reconstructed according to semantic relations. In this paper. IT-People Event Ontology is constructed using people information extracted from web portals. IT-People Event Ontology represents constant information and time-temporal information on people. A system using this ontology outputs the well-organized reconstructed information on a specific individual in interest, and then the reconstructed information is suitable for users' demand.

Ontology for Supplier Discovery in Manufacturing Domain (제조산업에서 공급기업 발굴을 위한 온톨로지)

  • Jung, Ki-Wook;Lee, Jae-Hun;Koh, In-Young;Joo, Jae-Koo;Cho, Hyun-Bo
    • IE interfaces
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    • v.25 no.1
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    • pp.31-39
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    • 2012
  • Discovering the suppliers capable of manufacturing the parts that satisfy buyer requirements via current online market places remains difficult due to semantic differences between what the suppliers can produce and what the buyer wants to acquire. One of the promising approaches to overcome the semantic difference is to adopt an ontology to describe the suppliers' manufacturing capabilities and the buyer requirements that range widely from manufacturing costs to eco-friendly design. Such an ontology dedicated to supplier discovery has yet to be developed. MSDL(Manufacturing Service Description Language) provides the basis for defining terms and their relationships in the ontology. Thus, the objective of this paper is to extend MSDL into a new ontology suitable for supplier discovery in mold manufacturing industry. In addition, a new ontology development method for supplier discovery will be proposed. Finally prototype demonstrations are provided to show a feasibility of the proposed ontology in mold manufacturing domains.

A Study on Tax Ontology Construction (조세 온톨로지 구축에 관한 연구)

  • Chang, Inho
    • Journal of Korean Library and Information Science Society
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    • v.44 no.1
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    • pp.385-408
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    • 2013
  • The purpose of this study is to build the tax ontology which can be used to manage imposables by the state or local governments. In this, the tax and related concepts were analyzed and then concept hierarchy i.e., taxonomies were formed. Especially, in the concept hierarchy, after multiple inherits were decomposed as 'primitive concepts' and then Rector's 'methodology of ontology implementation normalization', in which defined concepts were recombined, was used. The methodology employed was that the tax system, which was entangled with the direct taxes, local taxes, and property taxes that has multiple-inherits, was expressed explicitly and logically. After that, automatic classification was carried out through the inference engine, consistency was verified. Finally, some practical cases of ontology created were enumerated.

Incorporation of Fuzzy Theory with Heavyweight Ontology and Its Application on Vague Information Retrieval for Decision Making

  • Bukhari, Ahmad C.;Kim, Yong-Gi
    • International Journal of Fuzzy Logic and Intelligent Systems
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    • v.11 no.3
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    • pp.171-177
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    • 2011
  • The decision making process is based on accurate and timely available information. To obtain precise information from the internet is becoming more difficult due to the continuous increase in vagueness and uncertainty from online information resources. This also poses a problem for blind people who desire the full use from online resources available to other users for decision making in their daily life. Ontology is considered as one of the emerging technology of knowledge representation and information sharing today. Fuzzy logic is a very popular technique of artificial intelligence which deals with imprecision and uncertainty. The classical ontology can deal ideally with crisp data but cannot give sufficient support to handle the imprecise data or information. In this paper, we incorporate fuzzy logic with heavyweight ontology to solve the imprecise information extraction problem from heterogeneous misty sources. Fuzzy ontology consists of fuzzy rules, fuzzy classes and their properties with axioms. We use Fuzzy OWL plug-in of Protege to model the fuzzy ontology. A prototype is developed which is based on OWL-2 (Web Ontology Language-2), PAL (Protege Axiom Language), and fuzzy logic in order to examine the effectiveness of the proposed system.

Ontology for Semantic Retrieval of MPEG-7 MDS and TV-Anytime Multimedia Data (멀티미디어 데이터의 의미적 검색을 위한 MPEG-7 MDS 와 TV-Anytime 기반 온톨로지)

  • Song Chull-Hwan;Yoo Seong-Joon
    • Journal of Broadcast Engineering
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    • v.11 no.1
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    • pp.42-53
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    • 2006
  • This paper describes how to compose multimedia ontology for integrating/searching different types of multimedia databases. For this, we build integrated ontology based on MPEG-7 Multimedia Description Schemes (MDS), which is a representative standard for specifying multimedia contents, and the concept of TV-Anytime and re-express it using Web Ontology Language (OWL). In addition, we explain interoperability of the developed integrated ontology with other types of ontology with different concepts. Lastly, this paper describes the method of semantic search and retrieval using the integrated multimedia ontology.