• 한국산업정보학회:학술대회논문집
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• 한국산업정보학회 2007년도 춘계학술대회
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• pp.48-52
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• 2007

As huge amount of literature including biological data is being generated after post genome era, it becomes difficult for researcher to find useful knowledge from the biological databases. Bio-text mining and related natural language processing technique are the key issues in the intelligent knowledge retrieval from the biological databases. We propose a bio-text mining technique for the biologists who find Knowledge from the huge literature. At first, web robot is used to extract and transform related literature from remote databases. To improve retrieval speed, we generate an inverted file for keywords in the literature. Then, text mining system is used for extracting given knowledge patterns and keywords. Finally, we construct a grid computing environment to guarantee processing speed in the text mining even for huge literature databases. In the real experiment for 10,000 bio-literatures, the system shows 95% precision and 98% recall.

• 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.

• 한국비블리아학회지
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• 제26권1호
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• pp.217-231
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• 2015

본 연구에서는 췌장암의 유전자-단백질 상호작용 네트워크를 구성하고, 관련 연구에서 주요하게 언급되는 유전자-단백질의 유발관계 사슬을 파악함으로써, 췌장암의 원인을 규명하는 실증적인 연구로 이어질 수 있는 미발견 공공 지식을 제공하려 하였다. 이를 위하여 텍스트마이닝과 주경로 분석을 Swanson의 ABC 모델에 적용해 중간 개념인 B를 방향성을 가진 다단계 모델로 확장하고 가장 의미 있는 경로를 도출하였다. 본 연구의 주제가 된 췌장암의 사례처럼 시작점과 끝점조차 한정할 수 없는 미발견 공공 지식 추론에서 주경로 분석은 유용한 도구가 될 수 있을 것이다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.86-94
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• 2003

Electronically available biological literature has been accumulated exponentially in the course of time. So, researches on automatically acquiring knowledge from these tremendous data by text mining technology become more and more prosperous. However, most of the previous researches are technology oriented and are not well focused in practical extraction target, hence result in low performance and inconvenience for the bio-researchers to actually use. In this paper, we propose a more biology oriented target domain specific text mining system, that is, POSTECH bio-text mining system (POSBIOTM), for signal transduction pathway extraction, especially for G protein-coupled receptor (GPCR) pathway. To reflect more domain knowledge, we specify the concrete target for pathway extraction and define the minimal pathway domain ontology. Under this conceptual model, POSBIOTM extracts interactions and entities of pathways from the full biological articles using a machine learning oriented extraction method and visualizes the pathways using JDesigner module provided in the system biology workbench (SBW) [14]

• BMB Reports
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• 제56권11호
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• pp.594-599
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• 2023

A number of therapeutic drugs have been developed from functional chemicals found in plants. Knowledge of plants used for medicinal purposes has historically been transmitted by word of mouth or through literature. The aim of the present study is to provide a systemic platform for the development of lead compounds against breast cancer based on a traditional medical text. To verify our systematic approach, integrating processes consisted of text mining of traditional medical texts, 3-D virtual docking screening, and in vitro and in vivo experimental validations were demonstrated. Our text analysis system identified rutin as a specific phytochemical traditionally used for cancer treatment. 3-D virtual screening predicted that rutin could block EGFR signaling. Thus, we validated significant anti-cancer effects of rutin against breast cancer cells through blockade of EGFR signaling pathway in vitro. We also demonstrated in vivo anti-cancer effects of rutin using the breast cancer recurrence in vivo models. In summary, our innovative approach might be proper for discovering new phytochemical lead compounds designing for blockade of malignant neoplasm including breast cancer.

• Genomics & Informatics
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• 제17권2호
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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.

• 한국문헌정보학회지
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• 제50권2호
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• pp.289-307
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• 2016

에볼라 바이러스(Ebola virus disease)와 같은 전염병들은 사회적으로 큰 이슈가 되어 언론의 관심을 받으며 동시에 많은 연구의 대상이 되기도 한다. 이에 따라 국내외로 전염병과 관련된 텍스트 마이닝 연구가 활발하게 진행되고 있으나, 텍스트 마이닝 기법을 사용하여 상이한 특성을 가진 매체 간 주제를 분석한 연구는 아직까지 진행되지 않고 있다. 따라서 본 연구에서는 전염병 중 하나인 에볼라를 키워드로 하여 사회적 특성을 지닌 뉴스 기사와 바이오 분야의 전문적 특성을 지닌 연구 논문 간의 주제 분석을 진행하였다. 텍스트 분석에는 매체별 문헌 데이터로부터 다양한 토픽들을 추출하기 위해 토픽모델링 기법을 적용하였고, 매체 간의 구체적인 내용 분석을 위해 중요 개체를 선정하고 이를 중심으로 동시출현 단어 네트워크 분석을 수행하였다. 또한 각 매체별로 등장하는 주제를 시각적으로 표현하기 위해 토픽맵을 구축하였다. 분석 결과, 두 매체에서 다루는 주제의 차이점과 공통점을 발견할 수 있었으며 동시 출현 주제의 시계열 분석을 통해 매체 간 특성의 차이를 찾을 수 있었다. 본 연구를 통해 상이한 특성을 지닌 매체들의 주제와 개체들을 함께 제시하고, 매체 간의 공통점과 차이점을 보여줌으로써 매체별 정보 생산자들이 연구 및 현상 분석을 진행하는 데 있어 관점의 다양성을 제공할 수 있을 것이다.

• Genomics & Informatics
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• 제9권1호
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• pp.37-38
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• 2011

Biobank Impact Factor (BIF), which is a very effective criterion to evaluate the activity of biobanks, can be estimated by the citation information of biobanks from scientific papers. We have developed a program, ManBIF, to investigate the citation information from PDF files in the literature. The program manages a dictionary for expressions to represent biobanks and their resources, mines the citation information by converting PDF files to text files and searching with a dictionary, and produces a statistical report file. It can be used as an important tool by biobanks.

• 한국콘텐츠학회논문지
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• 제21권10호
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• pp.67-77
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• 2021

본 연구는 충청북도 정보화 계획수립 과정에서 지역의 특성을 반영하기 위해 텍스트마이닝의 토픽모델링, 연관분석, 감성분석을 진행하였다. 분석결과 충청북도는 상대적으로 정보격차 해소를 위해 교육분야를 중심으로 상대적으로 많은 활동을 하고 있으며, 비대면 서비스, 언택트 행정, 도시와 농촌 간 격차 해소를 위한 인프라 개선에 관심을 가지는 것으로 분석되었다. 아울러 지역 전략 산업에서 바이오와 IT 결합에 긍정적인 평가를 하고 있으며, 타지역 IT서비스 혁신사례 도입, IT 기업과 협력을 통한 스마트시티 구축, 정치적 이슈와 연관되지 않는 위기관리가 필요하다는 점을 확인하였다. 본 연구는 충청북도 정보화 추진과정에서 지역의 변화 흐름과 이슈를 구체적으로 파악하는 방안으로 활용될 수 있을 것이다.

• 한국응용과학기술학회지
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• 제37권1호
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• pp.76-82
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• 2020

Big data analysis in healthcare research seems to be a necessary strategy for the convergence of sports science and technology in the era of the Fourth Industrial Revolution. The purpose of this study is to provide the basic review to secure the diversity of big data and healthcare convergence by discussing the concept, analysis method, and application examples of big data and by exploring the application. Text mining, data mining, opinion mining, process mining, cluster analysis, and social network analysis is currently used. Identifying high-risk factor for a certain condition, determining specific health determinants for diseases, monitoring bio signals, predicting diseases, providing training and treatments, and analyzing healthcare measurements would be possible via big data analysis. As a further work, the big data characteristics provide very appropriate basis to use promising software platforms for development of applications that can handle big data in healthcare and even more in sports science.