• Genomics & Informatics
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• v.19 no.3
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• pp.27.1-27.4
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• 2021

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural language understanding. Biological named entity recognition (NER) and named entity normalisation (NEN) are two common tasks aiming at identifying and linking biologically important entities such as genes or gene products mentioned in the literature to biological databases. In this paper, we present an updated version of OryzaGP, a gene and protein dataset for rice species created to help natural language processing (NLP) tools in processing NER and NEN tasks. To create the dataset, we selected more than 15,000 abstracts associated with articles previously curated for rice genes. We developed four dictionaries of gene and protein names associated with database identifiers. We used these dictionaries to annotate the dataset. We also annotated the dataset using pretrained NLP models. Finally, we analysed the annotation results and discussed how to improve OryzaGP.

• Journal of Sasang Constitutional Medicine
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• v.29 no.3
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• pp.242-247
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• 2017

Objective Korean medicine Data Center (KDC) has established large-scale biological and clinical data based on Korean medicine to demonstrate and validate its theory. The aim of this study was to develop KDC teaching dataset and user guideline to improve utilization of the KDC. Method KDC teaching dataset were selected using stratified random sampling according to the Sasang constitution (SC). This dataset included 72 variables of 500 sample subjects. The user guideline described how to conducted eight statistical analysis methods using the teaching dataset. Results The KDC teaching dataset was sampled from 200(40%) Taeeumin, 125(25%) Soeumin, and 175(35%) Soyanain. It was consisted of questionnaire (basic, habit, disease, symptom), physical exam (body measurement, blood pressure), blood exam, and expert' SC diagnosis. The usage guidelines provided instruction for users to perform several statistical analysis step by step with KDC teaching dataset. Conclusion We hope that our results will contribute to enhancing KDC utilization and understanding.

• Genomics & Informatics
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• v.17 no.2
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• pp.17.1-17.3
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• 2019

Text mining has become an important research method in biology, with its original purpose to extract biological entities, such as genes, proteins and phenotypic traits, to extend knowledge from scientific papers. However, few thorough studies on text mining and application development, for plant molecular biology data, have been performed, especially for rice, resulting in a lack of datasets available to solve named-entity recognition tasks for this species. Since there are rare benchmarks available for rice, we faced various difficulties in exploiting advanced machine learning methods for accurate analysis of the rice literature. To evaluate several approaches to automatically extract information from gene/protein entities, we built a new dataset for rice as a benchmark. This dataset is composed of a set of titles and abstracts, extracted from scientific papers focusing on the rice species, and is downloaded from PubMed. During the 5th Biomedical Linked Annotation Hackathon, a portion of the dataset was uploaded to PubAnnotation for sharing. Our ultimate goal is to offer a shared task of rice gene/protein name recognition through the BioNLP Open Shared Tasks framework using the dataset, to facilitate an open comparison and evaluation of different approaches to the task.

• Journal of Biomedical Engineering Research
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• v.43 no.3
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• pp.131-135
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• 2022

Due to COVID-19, Correct method of wearing mask is important to prevent COVID-19 and the other respiratory tract infections. And the deep learning technology in the image processing has been developed. The purpose of this study is to create the type of mask wearing dataset for deep learning models and select the deep learning model to detect the wearing mask correctly. The Image dataset is the 2,296 images acquired using a web crawler. Deep learning classification models provided by tensorflow are used to validate the dataset. And Object detection deep learning model YOLOs are used to select the detection deep learning model to detect the wearing mask correctly. In this process, this paper proposes to validate the type of mask wearing datasets and YOLOv5 is the effective model to detect the type of mask wearing. The experimental results show that reliable dataset is acquired and the YOLOv5 model effectively recognize type of mask wearing.

• Genomics & Informatics
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• v.16 no.4
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• pp.39.1-39.3
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• 2018

The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-based association study of large-scale genetic dataset-namely, PHARAOH. However, researcher-level application of the PHARAOH method has been limited by a lack of generally used file formats and the absence of various quality control options that are essential to practical analysis. In order to overcome these limitations, we introduce our integration of the PHARAOH method into our recently developed all-in-one workbench. The proposed new PHARAOH program not only supports various de facto standard genetic data formats but also provides many quality control measures and filters based on those measures. We expect that our updated PHARAOH provides advanced accessibility of the pathway-level analysis of large-scale genetic datasets to researchers.

• Genomics & Informatics
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• v.3 no.1
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• pp.30-34
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• 2005

Microarray technology makes it possible to measure the expressions of tens of thousands of genes simultaneously under various experimental conditions. Identifying differentially expressed genes in each single experimental condition is one of the most common first steps in microarray gene expression data analysis. Reasonable choices of thresholds for determining differentially expressed genes are used for the next-stap-analysis with suitable statistical significances. We present a supervised model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are trying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful structure from microarray datasets.

• Korean Journal of Biological Psychiatry
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• v.30 no.1
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• pp.24-30
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• 2023

Objectives Alzheimer's disease (AD) is the most common form of dementia in older adults, damaging the brain and resulting in impaired memory, thinking, and behavior. The identification of differentially expressed genes and related pathways among affected brain regions can provide more information on the mechanisms of AD. The aim of our study was to identify differentially expressed genes associated with AD and combined biomarkers among them to improve AD risk prediction accuracy. Methods Machine learning methods were used to compare the performance of the identified combined biomarkers. In this study, three publicly available gene expression datasets from the hippocampal brain region were used. Results We detected 31 significant common genes from two different microarray datasets using the limma package. Some of them belonged to 11 biological pathways. Combined biomarkers were identified in two microarray datasets and were evaluated in a different dataset. The performance of the predictive models using the combined biomarkers was superior to those of models using a single gene. When two genes were combined, the most predictive gene set in the evaluation dataset was ATR and PRKCB when linear discriminant analysis was applied. Conclusions Combined biomarkers showed good performance in predicting the risk of AD. The constructed predictive nomogram using combined biomarkers could easily be used by clinicians to identify high-risk individuals so that more efficient trials could be designed to reduce the incidence of AD.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.279-285
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• 2004

In the disease association study, the tagSNP selection problem is important at the view of time and cost. We developed the new tagSNP selection system that has also facilities for the haplotype reconstruction and missing data processing. In our system, we improved biological meanings using LD coefficients as well as dynamic programming method. And our system has capability of processing large -scale dataset, such as the total SNPs on a chromosome. We have tested our system with various dataset from daly et al., patil et al., HapMap Project, artificial dataset, and so on.

• Journal of Biomedical Engineering Research
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• v.41 no.1
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• pp.28-34
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• 2020

In this paper, we introduce motion artifact reduction algorithm for interleaved MRI using an advanced 3D approximation algorithm. The motion artifact framework of this paper is data corrected by post-processing with a new 3-D approximation algorithm which uses data structure for each voxel. In this study, we simulate and evaluate our algorithm using Shepp-Logan phantom and T1-MRI template for both scattered dataset and uniform dataset. We generated motion artifact using random generated motion parameters for the interleaved MRI. In simulation, we use image coregistration by SPM12 (https://www.fil.ion.ucl.ac.uk/spm/) to estimate the motion parameters. The motion artifact correction is done with using full dataset with estimated motion parameters, as well as use only one half of the full data which is the case when the half volume is corrupted by severe movement. We evaluate using numerical metrics and visualize error images.

• Genomics & Informatics
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• v.11 no.3
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• pp.135-141
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• 2013

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait ($p_{corr}$ < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.