Text mining for finding functional community of related genes using TCM knowledge

Authors:
Zhaohui Wu;Xuezhong Zhou;Baoyan Liu;Junli Chen
Affiliations:
Zhejiang University, Hangzhou, 310027, P.R.China;Zhejiang University, Hangzhou, 310027, P.R.China;China Academy of Traditional Chinese Medicine, Beijing 100700, P.R.China;Zhejiang University, Hangzhou, 310027, P.R.China
Venue:
PKDD '04 Proceedings of the 8th European Conference on Principles and Practice of Knowledge Discovery in Databases
Year:
2004

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Abstract

We present a novel text mining approach to uncover the functional gene relationships, maybe, temporal and spatial functional modular interaction networks, from MEDLINE in large scale. Other than the regular approaches, which only consider the reductionistic molecular biological knowledge in MEDLINE, we use TCM knowledge(e.g. Symptom Complex) and the 50,000 TCM bibliographic records to automatically congregate the related genes. A simple but efficient bootstrapping technique is used to extract the clinical disease names from TCM literature, and term co-occurrence is used to identify the disease-gene relationships in MEDLINE abstracts and titles. The underlying hypothesis is that the relevant genes of the same Symptom Complex will have some biological interactions. It is also a probing research to study the connection of TCM with modern biomedical and post-genomics studies by text mining. The preliminary results show that Symptom Complex gives a novel top-down view of functional genomics research, and it is a promising research field while connecting TCM with modern life science using text mining.