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http://dx.doi.org/10.5392/JKCA.2015.15.10.616

Implementing Biological Network Analysis System through Oriental Medical Literature Analysis  

Yu, Seok Jong (한국과학기술정보연구원 생명의료융합기술연구실)
Cho, Yongseong (한국과학기술정보연구원 생명의료융합기술연구실)
Lee, Junehawk (한국과학기술정보연구원 생명의료융합기술연구실)
Seo, Dongmin (한국과학기술정보연구원 생명의료융합기술연구실)
Yea, Sang-Jun (한국한의학연구원 K-herb연구단)
Kim, Chul (한국한의학연구원 K-herb연구단)
Publication Information
The Journal of the Korea Contents Association / v.15, no.10, 2015 , pp. 616-625 More about this Journal
Abstract
Currently, oriental medicine research is focused with modern research technology and validate it's various biochemical effect by combining with molecular biology technology. But there are few searching system for finding biochemical mechanism which is related to major compounds in oriental medicine. In this research, we aimed developing korean herb database based on text-mining system by analyzing PubMed data. We have developed prototype system for searching chemical, gene and biological relation in oriental medicine. It is characterized by modern oriental medicine research trend with major chemical, gene and protein information. Analysis results can be searched on the prototype system with visualization of the biological interactions.
Keywords
Oriental Medicine; Biological Network; Network Analysis; PubMed;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
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1 M. S. Sundrud, S. B. Koralov, M. Feuerer, D. P. Calado, A. E. Kozhaya, A. Rhule- Smith, R. E. Lefebvre, D. Unutmaz, R. Mazitschek, H. Waldner, M. Whitman, T. Keller, and A. Rao, "Halofuginone inhibits TH17 cell differentiation by activating the amino acid starvation response", Science, Vol.324, No.5932, pp.1334-1338, Jun. 2009.   DOI   ScienceOn
2 김상균, 박동훈, 김안나, 오용택, 김지영, 예상준, 김철, 장현철, "한의 온톨로지 기반 시맨틱 검색 시스템", 한국콘텐츠학회논문지, 제12권, 제12호, pp.533-543, 2012.   DOI
3 예상준, 양창섭, 김철, "헬스 2.0 기반의 한의정보 프레임워크 모델 설계", 한국콘텐츠학회논문지, 제13권, 제11호, pp.807-814, 2013.   DOI
4 Y. Feng, Z. Wu, X. Zhou, Z. Zhou, and W. Fan, "Knowledge discovery in traditional Chinese medicine: state of the art and perspectives", Artif Intell Med, Vol.38, No.3, pp.219-236, Nov. 2006.   DOI   ScienceOn
5 L. Hirschman, A. Yeh, C. Blaschke, and A. Valencia, "Overview of BioCreAtIvE: critical assessment of information extraction for biology", presented at the BMC bioinformatics, Vol.6, No.1, p.S1, 2005.
6 D. C. Hao and P. G. Xiao, "Network pharmacology: a Rosetta Stone for traditional Chinese medicine", Drug Dev. Res, Vol.75, No.5, pp.299-312, Aug. 2014.   DOI   ScienceOn
7 H. Kitano, "Systems biology: a brief overview", Science, Vol.295, No.5560, pp.1662-1664, Mar. 2002.   DOI   ScienceOn
8 J. Fluck and M. Hofmann-Apitius, "Text mining for systems biology", Drug Discov. Today, Sep. 2013.
9 B. Settles, "ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text", Bioinformatics, Vol.21, No.14, pp.3191-3192, Jul. 2005.   DOI   ScienceOn
10 R. Leaman and G. Gonzalez, "BANNER: an executable survey of advances in biomedical named entity recognition", Pac Symp Biocomput, pp.652-663, 2008.
11 D. M. Jessop, S. E. Adams, E. L. Willighagen, L. Hawizy, and P. Murray-Rust, "OSCAR4: a flexible architecture for chemical text-mining", J Cheminform, Vol.3, No.1, p.41, 2011.   DOI   ScienceOn
12 T. Ono, H. Hishigaki, A. Tanigami, and T. Takagi, "Automated extraction of information on protein-protein interactions from the biological literature", Bioinformatics, Vol.17, No.2, pp.155-161, Feb. 2001.   DOI   ScienceOn
13 Y. Hao, X. Zhu, M. Huang, and M. Li, "Discovering patterns to extract protein-protein interactions from the literature: Part II.", Bioinformatics, Vol.21, No.15, pp.3294-3300, Aug. 2005.   DOI   ScienceOn
14 J. Ren, N. Williams, L. Clementi, S. Krishnan, and W. W. Li, "Opal web services for biomedical applications", Vol.38, No.Web Server, pp.W724-W731, Jun. 2010.   DOI
15 X. Zhou, B. Liu, Z. Wu, and Y. Feng, "Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks", Artif Intell Med, Vol.41, No.2, pp.87-104, Oct. 2007.   DOI   ScienceOn
16 Y. C. Fang, H. C. Huang, H. H. Chen, and H. F. Juan, "TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining", BMC Complement Altern Med, Vol.8, p.58, 2008.   DOI   ScienceOn
17 B. Kemper, T. Matsuzaki, Y. Matsuoka, Y. Tsuruoka, H. Kitano, S. Ananiadou, and J. Tsujii, "PathText: a text mining integrator for biological pathway visualizations", Bioinformatics, Vol.26, No.12, pp.i374-81, Jun. 2010.   DOI   ScienceOn
18 M. S. D. L. Ali Z Ijaz, "MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge", BMC Bioinformatics, Vol.11, No.2, p.S3, 2010.
19 http://sourceforge.net/projects/jeutils
20 Y. Wang, T. Suzek, J. Zhang, J. Wang, S. He, T. Cheng, B. A. Shoemaker, A. Gindulyte, and S. H. Bryant, "PubChem BioAssay: 2014 update", Vol.42, No.Database issue, pp.D1075-82, Jan. 2014.
21 http://processingjs.org/