PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine

Ji-Hyun Lee; Kyoung Mii Park; Dong-Jin Han; Nam Young Bang; Do-Hee Kim; Hyeongjin Na; Semi Lim; Tae Bum Kim; Dae Gyu Kim; Hyun-Jung Kim; Yeonseok Chung; Sang Hyun Sung; Young-Joon Surh; Sunghoon Kim; Byung Woo Han

doi:10.1371/journal.pone.0142624

PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine

PLoS One. 2015 Nov 10;10(11):e0142624. doi: 10.1371/journal.pone.0142624. eCollection 2015.

Authors

Ji-Hyun Lee^{1

2

3}, Kyoung Mii Park^{2

3}, Dong-Jin Han^{1

4}, Nam Young Bang^{1

4}, Do-Hee Kim², Hyeongjin Na², Semi Lim¹, Tae Bum Kim², Dae Gyu Kim¹, Hyun-Jung Kim⁵, Yeonseok Chung², Sang Hyun Sung², Young-Joon Surh², Sunghoon Kim^{1

4}, Byung Woo Han^{2

3}

Affiliations

¹ Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152-742, Republic of Korea.
² Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
³ Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea.
⁴ Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
⁵ College of Pharmacy, Chung-Ang University, Seoul 156-756, Republic of Korea.

Abstract

Despite the growing attention given to Traditional Medicine (TM) worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM) database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound), disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software) and BioMart (a data federation framework) for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Database Management Systems*
Medicine, Traditional*
Republic of Korea
Systems Integration*

Grants and funding

This research was supported by the Basic Science Research Program funded by the Ministry of Education [JL] and Global Frontier Project funded by the Ministry of Science, ICT and Future Planning through the National Research Foundation of Korea [BH] (NRF-2013R1A1A2058353 and NRF-2013M3A6A4043695). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.