TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining

Abstract

Background: Traditional Chinese Medicine (TCM), a complementary and alternative medical system in Western countries, has been used to treat various diseases over thousands of years in East Asian countries. In recent years, many herbal medicines were found to exhibit a variety of effects through regulating a wide range of gene expressions or protein activities. As available TCM data continue to accumulate rapidly, an urgent need for exploring these resources systematically is imperative, so as to effectively utilize the large volume of literature.

Extraction of ObjectProperty-UsageMethod Relation from Web Documents

“…However, unlike our research, the semantic relations extracted by previous researches [4,5,[7][8][9] mostly occurred within one sentence containing either the relation between two NPs (NP1 and NP2 of a sentence expression(S) as S NP1 VP; VP verb NP2 |…) or the relation between NP1 and VP.…”

“…In 2008, [4] presented TCMGeneDIT, a database that provides associations on Traditional Chinese Medicine (TCM), genes, diseases, the effects of TCM, ingredients, and the TCM effect and effecter relationships, which are mined and extracted from literature. The association discovery on noun phrases (TCM, disease, gene, ingredient, and effect) was conducted by using hypothesis testing and collocation analysis on annotated documents where a rule-based information extraction was performed.…”

“…Several strategies [4][5][6][7][8][9] have been proposed to determine the semantic relation from the textual data.…”

“…There are several techniques [4][5][6][7][8][9] that have been used to extract the semantic relations involved with the object properties and the procedural knowledge based on explanations from documents (see Section 2) whilst the other previous researches [10] on the semantic relation determination from texts relies on the relations, i.e. is-a, part-of, and cause-effect, between two entities of noun phrases without boundary consideration.…”

Association Rules Mining and Statistic Test over Multiple Datasets on TCM Drug Pairs

“…Both computational and experimental efforts have been made to relate the TCM components to those of modern medicine, in order to demonstrate the effectiveness and mechanisms of TCM scientifically. As the basis for data mining, some TCM databases has been developed including chemical ingredients, pharmacological information and 3D structure [1][2][3].…”