• Journal of KIISE:Software and Applications
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• v.31 no.12
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• pp.1602-1610
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• 2004

As various genome projects have produced enormous amount of biosequence data, functional sequence analysis in terms of tile nucleic acid and protein becomes very significant. In functional genomics and proteomics, the functional analysis of each individual gene and protein remains a big challenge. Contrary to traditional studies, which regard proteins as not components of a whole protein interaction network but individual entities, recent studies have focused on examining functions and roles of each individual gene and protein in view of a whole life system. In this regard, it has been recognized as an appropriate method to analyze protein function on the basis of synthetic information of its interaction and domain modularity. In this context, this paper introduces the PIVS (Protein-protein interaction Inference & Visualization System), which predicts the interaction relationship of input proteins by taking advantage of information on homology degree, domain modules which input sequences contain, and protein interaction relationship. The information on domain modules can increase the accuracy of the function and interaction relationship analysis in terms of the specificity and sensitivity.

• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.289-291
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• 2004

본 논문에서는 생물체의 세포 내에 존재하는 방대한 객체들 사이의 복잡한 관계들로 표현되는 상호작용 네트워크를 효율적으로 구축할 수 있는 시스템을 제안한다. 이 시스템은 바이오 도메인 지식을 사용하여 상호작용 네트워크를 관리 및 활용하기 쉽도록 구축하고, 단백질과 같은 단순 바이오 객체뿐만 아니라 여러 개의 바이오 객체들로 구성된 복합 객체도 관리 할 수 있다. 여기서, 사용자가 바이오 객체들과 이들간의 복잡한 상호작용 관계를 직관적으로 정의 할 수 있는 인터페이스를 제공한다. 또한, 정의된 객체 및 상호작용 관계 정보를 이용하여 바이오 네트워크를 개념적으로 단순하게 표현할 수 있으며, 시각적으로도 네트워크를 자동으로 최적화하여 사용자가 복잡한 네트워크를 쉽게 분석 할 수 있도록 지원한다.

• 한국HCI학회:학술대회논문집
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• 2007.02a
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• pp.932-937
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• 2007

생의학 분야 문헌의 양이 빠르게 증가함에 따라, 생의학 연구자들이 필요로 하는 정보를 얻기가 어렵게 되었다. 이를 해결하기 위해, 인간-컴퓨터 상호작용 분야에서는 생의학 문헌 검색 시스템, 또는 생의학 문헌의 정보 추출 시스템 등에 대한 연구가 진행되고 있다. 본 논문에서는 생의학 문헌으로부터 정보를 자동으로 추출하기 위한 관계정보 추출 시스템에 대해 소개한다. 소개하는 시스템은 크게 요약 수집 모듈, 관계 추출 모듈, 관계 가시화 모듈로 구성되어 있다. 우선, 요약 수집 모듈에서는 특정 주제의 문헌들을 검색 및 수집한다. 그리고, 관계 추출 모듈에서는 수집된 문헌들에 대해서, 단백질/유전자 등의 생물학 개체를 인식하고, 구문분석을 통하여 인식된 개체들 사이의 관계를 추출한다. 마지막으로, 관계 가시화 모듈에서는 추출된 관계를 통합하여 네트워크 형태로 가시화한다. 이 시스템은 생물학 실험 이전의 문헌 기반 타당성 검사, 단백질-단백질 상호작용 또는 특정 질병과 유전자의 조절관계 분석, 또는 대용량 문헌 처리를 통한 패스웨이 데이터베이스 구축 등에 활용될 수 있다.

• Proceedings of the Korea Information Processing Society Conference
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• 2022.11a
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• pp.63-65
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• 2022

DDI(Drug-Drug Interaction)는 병원에서 발생하는 약물이상반응의 30%를 유발하는 부작용이지만, 현실적으로 모든 약물쌍의 DDI 를 기존 in vivo, in vitro 방식으로 예측하는 것은 불가능하다. 그렇기에, 다양한 in silico 방식의 DDI 예측 모델이 연구되고 있다. 본 연구에서는, 단백질 네트워크 상에서 RWR(Random Walk with Restart) 알고리즘을 통해 약물과 직접적으로 상호작용하는 단백질과 간접적으로 상호작용하는 단백질의 정보를 사용하여 DDI 를 예측하는 모델을 개발하였다. 이 모델을 통하여 기존에 발견하지 못한 DDI 를 새롭게 발견하고, 신약 개발 시에도, 신약과 함께 복용 시 문제를 일으킬 수 있는 약물을 예측하여 약물 이상반응을 방지하고자 한다.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.1
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• pp.78-85
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• 2019

Membrane proteins are involved in many common diseases, including heart disease and cancer. In various disease states, such as cancer, abnormal signaling pathways that are related to the membrane proteins cause the cells to divide out of control and the expression of membrane proteins can be altered. Membrane proteins have the hydrophobic environment of a lipid bilayer, which makes an analysis of the membrane proteins notoriously difficult. Therefore, this study evaluated the efficacy of two different methods for optimal membrane protein extraction. High-speed centrifuge and reagent-based method with a -/+ filter aided sample preparation (FASP) were compared. As a result, the high-speed centrifuge method is quite effective in analyzing the mitochondrial inner membranes, while the reagent-based method is useful for endoplasmic reticulum membrane analysis. In addition, the function of the membrane proteins extracted from the two methods were analyzed using GeneGo software. GO processes showed that the endoplasmic reticulum-related responses had higher significance in the reagent-based method. An analysis of the process networks showed that one cluster in the high-speed centrifuge method and four clusters in the reagent-based method were visualized. In conclusion, the two methods are useful for the analysis of different subcellular membrane proteins, and are expected to assist in selecting the membrane protein extraction method by considering the target subcellular membrane proteins for study.

• KIISE Transactions on Computing Practices
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• v.23 no.3
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• pp.194-198
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• 2017

In this paper, we propose a revised Deep Convolutional Neural Network (DCNN) model to extract Protein-Protein Interaction (PPIs) from the scientific literature. The proposed method has the merit of improving performance by applying various global features in addition to the simple lexical features used in conventional relation extraction approaches. In the experiments using AIMed, which is the most famous collection used for PPI extraction, the proposed model shows state-of-the art scores (78.0 F-score) revealing the best performance so far in this domain. Also, the paper shows that, without conducting feature engineering using complicated language processing, convolutional neural networks with embedding can achieve superior PPIE performance.

• Journal of Life Science
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• v.34 no.3
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• pp.179-190
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• 2024

Cannabis sativa is a plant widely cultivated worldwide and has been used as a material for food, medicine, building materials and cosmetics. In this study, we assessed the functional effects of C. sativa stem and root extracts using network pharmacology and confirmed their novel functions. The components in stem and root ethanol extracts were identified by gas chromatography-mass spectrometry analysis, and networks between the components and proteins were constructed using the STICHI database. Functional annotation of the proteins was performed using the KEGG pathway. The effects of the extracts were confirmed in lysophosphatidylcholine-induced THP-1 cells using real-time PCR. A total of 21 and 32 components were identified in stem and root extracts, respectively, and 147 and 184 proteins were linked to stem and root components, respectively. KEGG pathway analysis showed that 69 pathways, including the MAPK signaling pathway, were commonly affected by the extracts. Further investigation using pathway networks revealed that terpenoid backbone biosynthesis was likely affected by the extracts, and the expression of the MVK and MVD genes, key proteins in terpenoid backbone biosynthesis, was decreased in LPC-induced THP-1 cells. Therefore, this study determined the diverse function of C. sativa extracts, providing information for predicting and researching the effects of C. sativa.

• Journal of KIISE:Databases
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• v.30 no.6
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• pp.573-584
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• 2003

Recent massive data generation by genomics and proteomics requires bioinformatic tools to extract the biological meaning from the massive results. Here we introduce ROSPath, a database system to deal with information on reactive oxygen species (ROS)-mediated cell signaling pathways. It provides a structured repository for handling pathway related data and tools for querying, displaying, and analyzing pathways. ROSPath data model provides the extensibility for representing incomplete knowledge and the accessibility for linking the existing biochemical databases via the Internet. For flexibility and efficient retrieval, hierarchically structured data model is defined by using the object-oriented model. There are two major data types in ROSPath data model: ‘bio entity’ and ‘interaction’. Bio entity represents a single biochemical entity: a protein or protein state involved in ROS cell-signaling pathways. Interaction, characterized by a list of inputs and outputs, describes various types of relationship among bio entities. Typical interactions are protein state transitions, chemical reactions, and protein-protein interactions. A complex network can be constructed from ROSPath data model and thus provides a foundation for describing and analyzing various biochemical processes.

• Journal of the Korean BIBLIA Society for library and Information Science
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• v.26 no.1
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• pp.217-231
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• 2015

This study aims to infer the gene-protein 'brings_about' chains of pancreatic cancer which were referred to in the pancreatic cancer related researches by constructing the gene-protein interaction network of pancreatic cancer. The chains can help us uncover publicly unknown knowledge that would develop as empirical studies for investigating the cause of pancreatic cancer. In this study, we applied a novel approach that grafts text mining and the main path analysis into Swanson's ABC model for expanding intermediate concepts to multi-levels and extracting the most significant path. We carried out text mining analysis on the full texts of the pancreatic cancer research papers published during the last ten-year period and extracted the gene-protein entities and relations. The 'brings_about' network was established with bio relations represented by bio verbs. We also applied main path analysis to the network. We found the main direct 'brings_about' path of pancreatic cancer which includes 14 nodes and 13 arcs. 9 arcs were confirmed as the actual relations emerged on the related researches while the other 4 arcs were arisen in the network transformation process for main path analysis. We believe that our approach to combining text mining analysis with main path analysis can be a useful tool for inferring undiscovered knowledge in the situation where either a starting or an ending point is unknown.

• Proceedings of the Korea Contents Association Conference
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• 2015.05a
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• pp.231-232
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• 2015

최근 유전체학, NGS(Next Generation Sequencing) 기술, IT/NT 장비의 발전 등에 따라 방대한 양의 바이오-메디컬 데이터가 생산되고, 이에 따라 빅데이터를 활용한 헬스케어 산업이 급속히 발달하고 있으며, 이와 관련된 빅데이터 기술은 국민의 건강 증대와 건강한 고령 삶을 제공하는 핵심 기술로 급부상하고 있다. 패스웨이는 단백질, 유전자, 세포 등의 생체적 요소 간의 역학관계 혹은 상호작용 등을 네트워크 형식으로 표현한 생물학적 심층지식으로, 바이오-메디컬 빅데이터 분석에 있어서 널리 활용되고 있다. 하지만 패스웨이는 매우 다양한 형태를 갖고 용량이 매우 큰 빅데이터로 이를 분석하는데 많은 시간이 소요된다. 그래서 본 논문에서는 세계적으로 가장 우수하고 방대한 양의 패스웨이를 제공하는 KEGG 패스웨이 데이터베이스로부터 사용자가 관심 갖는 패스웨이만을 자동 수집하고 패스웨이 간 계층구조를 기반으로 네트워크를 구성 후, 해당 패스웨이 네트워크에 대한 클러스터링과 핵심 패스웨이 선정을 통해 패스웨이 간의 역학관계 또는 상호작용을 직관적으로 분석할 수 시스템을 제안했다.