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Chinese Medicine
Published in: Chinese Medicine 1/2017

Open Access 01-12-2017 | Research

Revealing topics and their evolution in biomedical literature using Bio-DTM: a case study of ginseng

Authors: Qian Chen, Ni Ai, Jie Liao, Xin Shao, Yufeng Liu, Xiaohui Fan

Published in: Chinese Medicine | Issue 1/2017

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Abstract

Background

Valuable scientific results on biomedicine are very rich, but they are widely scattered in the literature. Topic modeling enables researchers to discover themes from an unstructured collection of documents without any prior annotations or labels. In this paper, taking ginseng as an example, biological dynamic topic model (Bio-DTM) was proposed to conduct a retrospective study and interpret the temporal evolution of the research of ginseng.

Methods

The system of Bio-DTM mainly includes four components, documents pre-processing, bio-dictionary construction, dynamic topic models, topics analysis and visualization. Scientific articles pertaining to ginseng were retrieved through text mining from PubMed. The bio-dictionary integrates MedTerms medical dictionary, the second edition of side effect resource, a dictionary of biology and HGNC database of human gene names (HGNC). A dynamic topic model, a text mining technique, was used to emphasize on capturing the development trends of topics in a sequentially collected documents. Besides the contents of topics taken on, the evolution of topics was visualized over time using ThemeRiver.

Results

From the topic 9, ginseng was used in dietary supplements and complementary and integrative health practices, and became very popular since the early twentieth century. Topic 6 reminded that the planting of ginseng is a major area of research and symbiosis and allelopathy of ginseng became a research hotspot in 2007. In addition, the Bio-DTM model gave an insight into the main pharmacologic effects of ginseng, such as anti-metabolic disorder effect, cardioprotective effect, anti-cancer effect, hepatoprotective effect, anti-thrombotic effect and neuroprotective effect.

Conclusion

The Bio-DTM model not only discovers what ginseng’s research involving in but also displays how these topics evolving over time. This approach can be applied to the biomedical field to conduct a retrospective study and guide future studies.
Appendix
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Metadata
Title
Revealing topics and their evolution in biomedical literature using Bio-DTM: a case study of ginseng
Authors
Qian Chen
Ni Ai
Jie Liao
Xin Shao
Yufeng Liu
Xiaohui Fan
Publication date
01-12-2017
Publisher
BioMed Central
Published in
Chinese Medicine / Issue 1/2017
Electronic ISSN: 1749-8546
DOI
https://doi.org/10.1186/s13020-017-0148-7

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