• Korean Journal of Computational Design and Engineering
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• v.20 no.2
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• pp.145-158
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• 2015

ISO 15926 is an international standard for the sharing and integration of plant lifecycle information. Plant design data consist of logical configuration, equipment specifications, 2D piping and instrument diagrams (P&IDs), and 3D plant models (shape data). Although 3D computer-aided design (CAD) data is very important data across the plant lifecycle, few studies on the exchange of 3D CAD data using ISO 15926 have been conducted so far. For this, we analyze information requirements regarding plant 3D design in the process industry. Based on the analysis, ISO 15926 templates are defined for the representation of constructive solid geometry (CSG) - based 3D design data. Since system environments for 3D CAD modeling and Semantic Web technologies are different from each other, we present system architecture for processing and visualizing plant 3D design data in the Web Ontology Language (OWL) format. Through the visualization test of ISO 15926-based 3D design data for equipment with a prototype system, feasibility of the proposed method is verified.

• Genomics & Informatics
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• v.3 no.3
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• pp.68-73
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• 2005

Pharmacogenomics research requires an intelligent integration of large-scale genomic and clinical data with public and private knowledge resources. We developed a web-based knowledge base for KPRN (Korea Pharmacogenomics Research Network, http://kprn.snubi. org/). Four major types of information is integrated; genetic variation, drug information, disease information, and literature annotation. Eighteen Korean pharmacogenomics research groups in collaboration have submitted 859 genotype data sets for 91 disease-related genes. Integrative analysis and visualization of the large collection of data supported by integrated biomedical path­ways and ontology resources are provided with a user-friendly interface and visualization engine empowered by Generic Genome Browser.

• Journal of Intelligence and Information Systems
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• v.21 no.4
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• pp.79-92
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• 2015

Knowledge map is widely used to represent knowledge in many domains. This paper presents a method of integrating the national R&D data and assists of users to navigate the integrated data via using a knowledge map service. The knowledge map service is built by using a lightweight ontology and a topic modeling method. The national R&D data is integrated with the research project as its center, i.e., the other R&D data such as research papers, patents, and reports are connected with the research project as its outputs. The lightweight ontology is used to represent the simple relationships between the integrated data such as project-outputs relationships, document-author relationships, and document-topic relationships. Knowledge map enables us to infer further relationships such as co-author and co-topic relationships. To extract the relationships between the integrated data, a Relational Data-to-Triples transformer is implemented. Also, a topic modeling approach is introduced to extract the document-topic relationships. A triple store is used to manage and process the ontology data while preserving the network characteristics of knowledge map service. Knowledge map can be divided into two types: one is a knowledge map used in the area of knowledge management to store, manage and process the organizations' data as knowledge, the other is a knowledge map for analyzing and representing knowledge extracted from the science & technology documents. This research focuses on the latter one. In this research, a knowledge map service is introduced for integrating the national R&D data obtained from National Digital Science Library (NDSL) and National Science & Technology Information Service (NTIS), which are two major repository and service of national R&D data servicing in Korea. A lightweight ontology is used to design and build a knowledge map. Using the lightweight ontology enables us to represent and process knowledge as a simple network and it fits in with the knowledge navigation and visualization characteristics of the knowledge map. The lightweight ontology is used to represent the entities and their relationships in the knowledge maps, and an ontology repository is created to store and process the ontology. In the ontologies, researchers are implicitly connected by the national R&D data as the author relationships and the performer relationships. A knowledge map for displaying researchers' network is created, and the researchers' network is created by the co-authoring relationships of the national R&D documents and the co-participation relationships of the national R&D projects. To sum up, a knowledge map-service system based on topic modeling and ontology is introduced for processing knowledge about the national R&D data such as research projects, papers, patent, project reports, and Global Trends Briefing (GTB) data. The system has goals 1) to integrate the national R&D data obtained from NDSL and NTIS, 2) to provide a semantic & topic based information search on the integrated data, and 3) to provide a knowledge map services based on the semantic analysis and knowledge processing. The S&T information such as research papers, research reports, patents and GTB are daily updated from NDSL, and the R&D projects information including their participants and output information are updated from the NTIS. The S&T information and the national R&D information are obtained and integrated to the integrated database. Knowledge base is constructed by transforming the relational data into triples referencing R&D ontology. In addition, a topic modeling method is employed to extract the relationships between the S&T documents and topic keyword/s representing the documents. The topic modeling approach enables us to extract the relationships and topic keyword/s based on the semantics, not based on the simple keyword/s. Lastly, we show an experiment on the construction of the integrated knowledge base using the lightweight ontology and topic modeling, and the knowledge map services created based on the knowledge base are also introduced.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.383-387
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• 2005

One of the most important issues in post-genome era is identifying functions of genes and understanding the interaction among them. Such interactions from complex biochemical pathways, which are very useful to understand the organism system. We present an integrated biochemical pathway database system with a set of software tools for reconstruction, visualization, and simulation of the pathways from the database. The novel features of the presented system include: (a) automatic integration of the heterogeneous biochemical pathway databases, (b) gene ontology for high quality of database in the integration and query (c) various biochemical simulations on the pathway database, (d) dynamic pathway reconstruction for the gene list or sequence data, (e) graphical tools which enable users to view the reconstructed pathways in a dynamic form, (f) importing/exporting SBML documents, a data exchange standard for systems biology.

• Proceedings of the CALSEC Conference
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• 2004.02a
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• pp.107-111
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• 2004

The purpose of the study is to develop an integrated knowledge management system for the domains of genome and nano-technology, in which terminology-based literature mining, knowledge acquisition, knowledge structuring, and knowledge retrieval are combined. The system supports integrating different types of databases (papers and patents, technologies and innovations) and retrieving different types of knowledge simultaneously. The main objective of the system is to facilitate knowledge acquisition from documents and new knowledge discovery through a terminology-based similarity calculation and a visualization of automatically structured knowledge. Implementation issue of the system is also mentioned.

• Proceedings of the Korean Information Science Society Conference
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• 2005.07b
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• pp.646-648
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• 2005

시맨틱 웹과 시맨틱 웹 서비스의 논리적 기반이 되는 온톨로지에 대한 연구가 활발히 진행되고 있다. W3C는 웹 온톨로지 기술을 위한 표준 언어로 OWL을 발표했고, OWL로 기술된 온톨로지는 웹 서비스, 유비쿼터스 컴퓨팅 등에서 활용되고 있다. 그러나 OWL의 복잡한 문법 구조는 OWL 온틀로지 개발을 어렵게 하고 있어, 직관적으로 OWL 온틀로지를 개발할 수 있는 방법이 요구되었고. 이를 위해 Protege 등 많은 온톨로지 편집기들이 개발되었다. 본 논문에서는 쉬운 OWL 온톨로지 편집을 위해 개체 중심의 온톨로지 시각화를 통한 온톨로지 편집기 개발에 관한 내용을 담고 있다. 이 편집기는 JDK 1.4 환경에서 개발되었으며 OWL 온톨로지 분석을 위해 Jena2 API를 사용하였다.

• The Journal of the Korea Contents Association
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• v.14 no.4
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• pp.418-424
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• 2014

This paper aim; to develop the National R&D Information Navigation System(NRnDINS) that is convenient and easy to use by the researchers on the basis of information filtering and visualization by converging and integrating the three types of the contents, namely, paper, report and project at the stage of development of the information system An information system is developed by establishing ontology and RDF on the three types of contents, and by applying information filtering and semantic search technology after having created the prototype for the screen by reflecting the user needs analysis and information visualization elements surveyed at the previous stage of information service planning. In this paper, to make the measure for information filtering, R&D navigation index is prosed and implemented, and NRnDINS capable of integrated search of the R&D contents through information visualization is developed. Also, for the testing of the developed system, the preference survey for its design by 1m persons and usability test of the system by 10 users are performed The result of the survey on the preference for the design is affirmative with 85% of the subjects finding it favorable and the composite receptivity is good with the score of 87.2 the results of the usability test. However, it was also found that further development of the personalization functions is needed. It is hoped that the R&D navigation index of the proposed and implemented in this paper would present quantitative objectivity and will induce further development of other information filtering index of contents in the future.

• Nutrition Research and Practice
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• v.14 no.4
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• pp.412-422
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• 2020

BACKGROUND/OBJECTIVES: This study investigates correlations between circulating microRNAs (miRNAs) and obesity-related parameters among young women (aged 20-30 years old) in Korea. SUBJECTS/METHODS: We analyzed TaqMan low density arrays (TLDAs) of circulating miRNAs in 9 lean (body mass index [BMI] < 25 kg/㎡) and 15 obese (BMI > 25 kg/㎡) women. We also performed gene ontology (GO) analyses of the biological functions of predicted miRNA target genes, and clustered the results using the database for annotation, visualization and integrated discovery. RESULTS: The TLDA cards contain 754 human miRNAs; of these, the levels of 8 circulating miRNAs significantly declined (> 2-fold) in obese subjects compared with those in lean subjects, including miR-1227, miR-144-5p, miR-192, miR-320, miR-320b, miR-484, miR-324-3p, and miR-378. Among them, miR-484 and miR-378 displayed the most significant inverse correlations with BMI (miR-484, r = -0.5484, P = 0.0056; miR-378, r = -0.5538, P = 0.0050) and visceral fat content (miR-484, r = -0.6141, P = 0.0014; miR-378, r = -0.6090, P = 0.0017). GO analysis indicated that genes targeted by miR-484 and miR-378 had major roles in carbohydrate and lipid metabolism. CONCLUSION: Our result showed the differentially expressed circulating miRNAs in obese subjects compared to lean subjects. Although the mechanistic study to reveal the causal role of miRNAs remains, these miRNAs may be novel biomarkers for obesity.

• Journal of Korean Neurosurgical Society
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• v.65 no.5
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• pp.697-709
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• 2022

Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

• Journal of Plant Biotechnology
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• v.50
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• pp.127-136
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• 2023

Water scarcity decreases the rate of photosynthesis and, consequently, the yield of banana plants (Musa spp). In this study, transcriptome analysis was performed to identify photosynthesis-related genes in banana plants and determine their expression profiles under water stress conditions. Banana plantlets were in vitro cultured on Murashige and Skoog agar medium with and without 10% polyethylene glycol and marked as BP10 and BK. Chlorophyll contents in the plant shoots were determined spectrophotometrically. Two cDNA libraries generated from BK and BP10 plantlets, respectively, were used as the reference for transcriptome data. Gene ontology (GO) enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) and visualized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway prediction. Morphological observations indicated that water deficiency caused chlorosis and reduced the shoot chlorophyll content of banana plantlets. GO enrichment identified 52 photosynthesis-related genes that were affected by water stress. KEGG visualization revealed the pathways related to the 52 photosynthesisr-elated genes and their allocations in four GO terms. Four, 12, 15, and 21 genes were related to chlorophyll biosynthesis, the Calvin cycle, the photosynthetic electron transfer chain, and the light-harvesting complex, respectively. Differentially expressed gene (DEG) analysis using DESeq revealed that 45 genes were down-regulated, whereas seven genes were up-regulated. Four of the down-regulated genes were responsible for chlorophyll biosynthesis and appeared to cause the decrease in the banana leaf chlorophyll content. Among the annotated DEGs, MaPNDO, MaPSAL, and MaFEDA were selected and validated using quantitative real-time PCR.