Stress: Plant Protein Database
Frequently Asked Questions

1. What is PSPDB?

PSPDB: Plant Stress Protein Database is a repository of manually curated and experimentally validated plant proteins involved in abiotic and biotic stresses.   (Read on..)

2. How many entries are contained in PSPDB?

As on June 10, 2013, the database contains 2064 proteins experimentally validated in plants, which falls under abiotic and biotic stresses.

3. Why PSPDB is developed?

There is a dearth of curated plant stress data in public domain. The manually curated proteins have been through the use of several tools. These proteins can be used as training cases for researchers who would like to test their proteins. Furthermore, additional tools have been added to allow users to extend the value and utility of the database.

4. What is the purpose of using this database?

Researchers working on stress factors can easily trace for a protein involved by searching a keyword, protein name, type of stress factor, gene function. It could be useful for a protein of interest with unknown function by using NCBI BLAST 2.2.18 against database for predicting its function. The results further can be interpreted and candidates can be chosen for the wet-lab experiments.  (Read on..)

5. What is uniqueness in this database apart from other databases available on stress factors?

This database contains only reviewed proteins from UniProt and are curated manually by cross checking each entry with one reference article. It has both abiotic and biotic stress factor proteins from higher plants, which are not available in other databases.

6. How can I query and use PSPDB?

You can use “Search option” using any keywords or boolean expression. A wide gamut of tools and their APIs are embedded in the database for you to query upon your genes. Please feel free to play around with it.

7. Can I download the entire database?

Yes, the database adheres to Creative Commons/GPL. You may request the authors by sending a requisition on why and how you are going to use it.

8. When and how can I find the database is updated?

Please join the mailing list here.

9. Can I submit my own sequence?

Yes, you are welcome. We will curate the entry before it is hosted in the database. We will also acknowledge you for the same.

10. If my protein is already submitted in GenBank, can I find the protein linked to PSPDB?

We are trying to NCBI Linkout now. Although linking the queried sequence that we have in our database can be Linkout to NCBI, the reverse may not be possible for no, until the database lapses the beta version.

11. When I query my protein of interest, I get normalization/SQL error. Please help.

Please ensure that your port settings are good and are open for: 8080. You may mail sundarATbiocluesDOTorg for any queries, you have.

12. Can I link it to SOAP/WSDL architecture of my database?

Yes, very soon. We will be working on it.

13. Is there an Application Program Interface (API) for the database? This will allow us to link it to our webserver?

Yes, the database is currently a beta version. We will have an API of it for you to host it internally.

14. Is this database free to use? Is it Creative Commons/General Public License?

Yes, very much for that we adhere to CC/GPL.

15. Why is that when I query nitrogen deficient stress protein, I get some other unrelated proteins as hits?

It could be because the same gene might have a stress related/semantic entry linked to it.

16. Calcium-dependent protein kinases (CDPKs) are the kinases which sense the calcium concentration changes in plant cells. Assuming that one of my queried proteins have links to abiotic stress, can I predict the role in various stress responses of these kinases?

Yes, since these kinases are involved in signal transduction cascades under various stress response.

17. SUMO proteins are related to abiotic stress. Can I get first-hand information on what kind of other proteins are related to these stress conditions, viz. drought?

Yes, most of the proteins from oxidative stress, chitin related, ABF, etc., share information with SUMO proteins and regulate post translational modifications.

18. I want to be a part of your team and help you with annotation. Am I allowed?

You are most welcome.

19. Is your database compliant with Minimum Information for Bioinformatics Investigation (MIABI) standards?

Yes please. We are working on it.

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