HIT Manual

1. Search HIT
Users can search for herbs, ingredients and targets on the “Search” page. Herbs can be searched by Chinese name, Chinese characters or English name. Herbal ingredient can be searched by name, CAS number or Pubchem CID; Users can also provide compound structural formulae to obtain ingredients with similarity greater than 0.7 in the database. Target can be searched by protein name, gene symbol or Uniprot ID.

2. Browse HIT
Users can browse all data by clicking the “Browse” button in the navigation bar. The data includes herbs, ingredients, and targets.

3. Target-mining
HIT 2.0 provides an online target-suggesting and curation platform via text-mining technology. The latest PubMed abstracts involving potential targets will be auto-retrieved for the queried compounds. Compound name, MeSH ID and Pubchem ID can be submitted to retrieve potential targets. HIT 2.0 also supports batch searches, where one query is entered per line.

On the Target-mining results page, users can select the query term to view and download the corresponding results.

These abstracts contain possible targets, but false positives may exist. We strongly recommend users to manually check these results for greater accuracy by registering the online My-target curation system. Users can click on “Select results to My-target curation system” and, in the pop-up box, select the results to their own My-target list.

Once users register and append a list of targets, they can manually check the targets in the My-target curation system, without going to the “Target-mining” page, unless they want to retrieve potential targets of a new compound.

4. My-Target curation

• Pubmed ID: Reference (linkable).
  
• Compound Name: The Compound retrieved by users.
  
• Key Word: Possible types of interactions between one compound and one target.
  
Sentence: Key description of the interaction between one compound and one target.

• Gene/Protein: Potential target.
  
• Is this a compound target: The default is “NO”. After clicking “Yes”, 10 types of interactions are displayed. Users need to judge the interaction type by scanning the key description.
  
• Supplement: If there are other genes in the sentence that are also targets of the compound, they can be added.
  
• Previous: View previous record
  
• Submit: submit the review result and view the next record
  
• Download: users can download the reviewed results at any time.