• Genomics & Informatics
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• 제3권2호
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• pp.47-51
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• 2005

Molecular mechanisms of biological processes are typically represented as 'pathways' that have a graph­analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and the semantics is embedded implicitly. The kinds of interactions that connect biological entities are likewise diverse. Consequently, how to model or process pathway data is not a trivial issue. In this review article, we give an overview of the challenges in pathway database development by taking the INOH project as an example.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.388-391
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• 2005

The Protein Structural and Functional Conservation need a common language for data definition. With the help of common language provided by Protein Ontology the high level of sequence and functional conservation can be extended to all organisms with the likelihood that proteins that carry out core biological processes will again be probable orthologues. The structural and functional conservation in these proteins presents both opportunities and challenges. The main opportunity lies in the possibility of automated transfer of protein data annotations from experimentally traceable model organisms to a less traceable organism based on protein sequence similarity. Such information can be used to improve human health or agriculture. The challenge lies in using a common language to transfer protein data annotations among different species of organisms. First step in achieving this huge challenge is producing a structured, precisely defined common vocabulary using Protein Ontology. The Protein Ontology described in this paper covers the sequence, structure and biological roles of Protein Complexes in any organism.

• 한국경영과학회:학술대회논문집
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• 대한산업공학회/한국경영과학회 2002년도 춘계공동학술대회
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• pp.301-305
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• 2002

Bioinformatics can beexplained as the science of developing algorithms, applicatiou tools, and computer databases and so on, for the purpose of supporting and enhancing biological research. Bioinformatic information systems (BIS) typically handle large data sets and the amount of the data goes up exponentially. Another impediment to easy extraction and retrieval of genomic data in BIS is the need to access different sites for similar information. Recently. there has been some attempts to integrate bioinformatics data in the World Wide Web (WWW) among the bioinformatics community by the internet computing technology. However, the work to integrate bioinformatics data on a universal platform has some problems because of the lack of standard, terminologies, semantics, and ontologies about bioinformatics. In this paper, an XML-based BIS architecture is proposed as an integrated BIS framework. The XML and related technologies allow the creation of meaningful information tags to exchange data between various databases as a standard format, and to create more simple interfaces. This integrated BIS framework has bioinformatic architectural components which is used in the Corporate Information Factory (CIF) method.

• Interdisciplinary Bio Central
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• 제3권2호
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• pp.7.1-7.6
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• 2011

Background: Published manuscripts are the main source of biological knowledge. Since the manual examination is almost impossible due to the huge volume of literature data (approximately 19 million abstracts in PubMed), intelligent text mining systems are of great utility for knowledge discovery. However, most of current text mining tools have limited applicability because of i) providing abstract-based search rather than sentence-based search, ii) improper use or lack of ontology terms, iii) the design to be used for specific subjects, or iv) slow response time that hampers web services and real time applications. Results: We introduce an advanced text mining system called PubMine that supports intelligent knowledge discovery based on diverse bio-ontologies. PubMine improves query accuracy and flexibility with advanced search capabilities of fuzzy search, wildcard search, proximity search, range search, and the Boolean combinations. Furthermore, PubMine allows users to extract multi-dimensional relationships between genes, diseases, and chemical compounds by using OLAP (On-Line Analytical Processing) techniques. The HUGO gene symbols and the MeSH ontology for diseases, chemical compounds, and anatomy have been included in the current version of PubMine, which is freely available at http://pubmine.kobic.re.kr. Conclusions: PubMine is a unique bio-text mining system that provides flexible searches and analysis of biological entity relationships. We believe that PubMine would serve as a key bioinformatics utility due to its rapid response to enable web services for community and to the flexibility to accommodate general ontology.

• Genomics & Informatics
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• 제18권2호
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• pp.23.1-23.6
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• 2020

The Human Phenotype Ontology (HPO) is the de facto standard ontology to describe human phenotypes in detail, and it is actively used, particularly in the field of rare disease diagnoses. For clinicians who are not fluent in English, the HPO has been translated into many languages, and there have been four initiatives to develop Japanese translations. At the Biomedical Linked Annotation Hackathon 6 (BLAH6), a rule-based approach was attempted to determine the preferable Japanese translation for each HPO term among the candidates developed by the four approaches. The relationship between the HPO and Mammalian Phenotype translations was also investigated, with the eventual goal of harmonizing the two translations to facilitate phenotype-based comparisons of species in Japanese through cross-species phenotype matching. In order to deal with the increase in the number of HPO terms and the need for manual curation, it would be useful to have a dictionary containing word-by-word correspondences and fixed translation phrases for English word order. These considerations seem applicable to HPO localization into other languages.

• 한국환경보건학회지
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• 제49권4호
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• pp.201-209
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• 2023

Background: To describe domain knowledge consistently and precisely, the establishment of a controlled vocabulary, a so-called ontology, is essential. Internationally, the plant ontology (PO) in the ecology field has been developed for the anatomy and developmental stages of plants in English, Spanish, and Japanese, but there is no Korean version of the PO due to a lack of knowledge on standardization for Korean plants. Objectives: We aimed to establish a Korean plant ontology with core PO architectures. Methods: The latest ontology web language (OWL)-formatted raw version of the PO was collected from the PO consortium site. A formal workflow process and OWL file-handing tools for efficient Korean content development were conducted and executed. Results: The macro- and micro-perspective frameworks of the PO were presented by analyzing the upper model and the internal OWL-leveled physical structure, respectively. We developed and validated Korean knowledge content for a total of 1,957 classes included in the PO and transplanted them into an ontology modeling system. Conclusions: A Korean plant ontology was established for international harmonization through improved compatibility and data exchangeability with multilingual environmental and ecological knowledge bases.

• 한국정보과학회논문지:소프트웨어및응용
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• 제32권6호
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• pp.461-472
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• 2005

본 논문에서는 OWL(Web Ontology Language) 기반 그래픽 바이오 온톨로지 관리 시스템을 설계하고 구현하였다 이 시스템은 생물학 용어들 사이의 복잡한 의미 관계들로 구성되는 바이오 온톨로지를 본 논문에서 정의한 그래픽 표기를 이용하여 표현한다. 또한, 시각화된 환경에서 수행되는 상속과 역상 속 메커니즘은 이미 구축된 방대한 용어들 사이의 관계를 시스템이 구조적으로 파악할 수 있게 함으로써, 전문가가 새로 추가되는 용어에 대한 관계를 의미적으로 일관성 있게 반자동으로 구축할 수 있다. 구축된 온톨로지는 기본적으로 OWL로 기술되며, 다른 여러 표준 온톨로지 언어(RDF/RDFS, DAML+OIL 등)로 의미적 손실 없이 변환된다. 본 시스템의 중요한 특징은 OWL의 강력한 의미적 표현력과 이를 잘 정의할 수 있는 그래픽 표기법을 채택함으로써 시각화된 메커니즘을 통해 바이오 온톨로지를 정교하게 모델링할 수 있다는 점이다.