1. Introduction

HerDing is a search engine to recommend herbs to treat diseases using genes and chemicals by integrating existing several databases and a text mining approach. Currently, HerDing supports information for herb-chemical, chemical-gene, and herb-disease relations. In our system, 19,476 herb names, 16,762 gene names, and 6,655 chemical names are indexed. The main purpose of HerDing is to help researchers obtain new insights for finding new drugs. HerDing allows users to input a list of genes, a chemical, and a herb as described below.

For compatible browsers of HerDing, Google Chrome and Internet explorer are recommendable.

2. Statistics

* Herb–Chemical–Gene relationships        4,880,575  
Herb–Chemical relationships        88,217  
Chemical–Gene relationships        228,904  
Herb names    19,476  
Chemical names    6,655  
Gene names    16,762  

3. Overview of User Interface

3.1. Input

As briefly mentioned at introduction, HerDing largely consists of three types of input pages: (i) a list of genes (ii) a chemical (iii) a herb.

3.1.1 Input (Genes/Diseases)

The below picture shows the HerDing page for input for genes and diseases.

3.1.2 Input (Chemicals)

The below picture shows the input page for chemicals. Users can input a single chemical name to retrieve related-herbs and -target genes. HerDing currently provides 6,655 chemicals which can be found by clicking "A list of supported chemicals" button.

3.1.3 Input (Herbs)

The below picture shows the input page for herbs. Users can input a single herb name to retrieve related-chemicals and -target genes. Note that users should choose a single input box among three of them which are divided into Chinese name, English name, Latin name. The supported herb list can be checked by clicking "A list of supported herbs" button.

3.2. Output

When inputs are given to HerDing, HerDing will retrieve a result page and it is consist of three parts as follows: Your Input, Retrieved herbs (*summary), Detailed information. Each category is well explined below.

4. Downloading resources

Retrieved results are freely downloadable by clicking a button denoted as 'download this result(.tsv)' in the result page. Downloadable files are tsv-formatted which is a file extension for tab-delimited file. Each row are separated with '\t'(tab) so that you can easily manipulate them. You may want to download all data in HerDing from the following link: (Click here).