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1. Given a protein name, find all of comparisons which include the protein as a DEP.
2. Find all comparison in DEPD from some sample attributes.
3. Find all comparison in DEPD from PMID.
4. How to add a queriable URL in your Web site.

DEPD Submissions

1. How do I submit comparison data to DEPD ?

1. How can I download data from the DEPD database?
2. How can I build local DEPD database?
3. Is a license required to download and use the DEPD data and/or applications?

DEPD Querying and Usage

1. Given a protein name, find all of experiments which include the protein as a DEP.
   
   Solution: Click here to open Search by protein page. The page provides two table for inputting protein name and sequence. Now only UniProt protein ID or protein name are recommended for search. Other type entries (such as PIR: S42582) are permitted but may be result in a slowly query.
   
   
2. Find all comparison in DEPD from some sample attributions.
   
   Solution: Click here to open Search by sample page. When querying by sample classification, search scope can be narrowed down using more features, because the relationship among diverse features is conjunct (‘AND').
   
   
3. Find paper & comparison in DEPD using PMID.
   
   Solution: Click here to open Search by sample page which contains a table for PMID query.It is the fastest way to get data from DEPD if you know the paper's PMID and the DEPD has included its data. Another use case is to check whether manuscripts have been embodied by DEPD or not, when user want to submit data to DEPD.
   
   
4. How to add a queriable URL in your Web site.
   
   Solution: DEPD provides two types queriable URLs for protein name and PMID number.
   1) For protein names (e.g. P04792):
   http://protchem.hunnu.edu.cn/depd/pronamesearcher?proname=P04792
   2) For PMID numbers (e.g. 15221772): http://protchem.hunnu.edu.cn/depd/DEPD_Website/Searchanalysis/ExpViewer.jsp?id=15221772

DEPD Submissions

1. How do I submit comparison data to DEPD?
   
   Solution: To submit data to DEPD, you need to access the page for submission. More detailed descriptions of how to do it can be found here.

 

DEPD data and applications

1. How can I download data from the DEPD database?
   
   Solution: To download DEPD database you can click here to open download center. The entire database is freely available in various file formats after logon on the system.
   
   
2. How can I build local DEPD database ?
   
   Solution: Download DEPD database firstly. You can use DOM to extract data from XML file automatically.
   You can also load these flat files into MYSQL database using some SQL commands in console such as:
   1. MYSQL> use depd; (where depd is the database name)
   2. MYSQL>load data infile 'DEPs.txt' into table depd_deps; (using DEPs.txt as a example)
   Notice: In there, we assume that the file (DEPs.txt) locates on the same folder with depd database.
   
   
3. Is a license required to download and use the DEPD data and/or applications?
   
   Solution: There are no license conditions attached to the non-commercial use of the DEPD database. For commercial use, entries in DEPD are copyright and advance permission is required. Please contact with administrator www.hqyone@hotmail.com. While there are no license restrictions or costs involved with using DEPD academically, we welcome sponsorship. Please let us know if you are interested in supporting DEPD and/or DEPD-related projects by emailing us at liangsp@hunnu.edu.cn.