TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis

Abstract

As an alternative to modern western medicine, Traditional Chinese Medicine (TCM) is receiving increasingly attention worldwide. Great efforts have been paid to TCM's modernization, which tries to bridge the gap between TCM and modern western medicine. As TCM and modern western medicine share a common aspect at molecular level that the compound(s) perturb human's dysfunction network and restore human normal physiological condition, the relationship between compounds (in herb, refer to ingredients) and their targets (proteins) should be the key factor to connect TCM and modern medicine. Accordingly, we construct this Traditional Chinese Medicine Integrated Database (TCMID, http://www.megabionet.org/tcmid/), which records TCM-related information collected from different resources and through text-mining method. To enlarge the scope of the TCMID, the data have been linked to common drug and disease databases, including Drugbank, OMIM and PubChem. Currently, our TCMID contains ∼47 000 prescriptions, 8159 herbs, 25 210 compounds, 6828 drugs, 3791 diseases and 17 521 related targets, which is the largest data set for related field. Our web-based software displays a network for integrative relationships between herbs and their treated diseases, the active ingredients and their targets, which will facilitate the study of combination therapy and understanding of the underlying mechanisms for TCM at molecular level.

Figure 1.

Database structure. A–E: six data fields for prescription, herbs, ingredients, diseases, targets and drugs, respectively. 1–5: relationship used to connect each other. 1: prescription is composed of herbs. 2: herb contains ingredients. 3: ingredients can interact with targets. 4: drugs have identified targets. 5: targets may be the causes of disease.

Figure 2.

Herbal ingredient–target–disease network. Node: red triangle, herbal ingredient; blue circle, herbal ingredient’s target; yellow square, disease related to targets. Node size depends on its degree. Mouse over a node will display detailed information on the node.

Figure 3.

Herbal ingredient–protein interaction network. Node: red triangle, the ingredient used for the query; yellow triangle, herbal ingredient(s); blue circle, herbal ingredient’s targets. Node size depends on its degree. Mouse over a node will display detailed information for the node.

Figure 4.

Herbal ingredient–target–disease–drug network. Node: red triangle, herbal ingredient; green triangle, drug; yellow square, disease; blue circle, herbal ingredient’s targets. Node size is related to its degree. Mouse over a node will display detailed information for the node.