Frequently Asked Questions:

1) What are the differences between ATDB and other toxin databases?
2) Given a protein name, how can I find all annotations of them?
3) What is the Toxin Ontology? Why?
4) The view of Ontology looks complex, how to operate it?
5) How can I extract toxins preferred basic on function, structure as well species information?
6) How do I submit a suggestion or a new toxin to the database?
7) How can I download data from ATDB?
8) What is the expected update cycle of the database?
9) Why the database cannot work properly on my browsers?
10) What is the TO evidence codes?
11) Is a license required to download and use the ATDB data?

1) What are the differences between ATDB and other toxin databases?
The targets of ATDB are collecting all of animal toxins and constructing uniform classification/annotation systems for them. So the most differences of ATDB to other previous toxin databases are it is not limited within certain taxonomic groups and uses controlled terms to descript toxin functions.

2) Given a protein name, how can I find all annotations of them?
Solution: Go to Text search page, select the type of ID from list, and input the protein ID and them push the search button. Notice: the search engine allows a batch search with protein ID list in same type separated by split char “|?

3) What is the Toxin Ontology? Why?
The Toxin Ontology (TO) is a structured, controlled vocabularies for consistent descriptions of toxin function and characters. It contains four term spaces () and more than 700 distinct terms. In ATDB, all of toxins have been annotated by more than 7000 TO terms in total. A detailed introduction can be found here.

4) The view of Ontology looks complex, how to operate it?

Each TO namespace has a view for browsing. (1) They include a left tree and a right table. You can focus and expand the branches of the tree by clicking leafs (terms) and detail about the terms will be show in the table. (2) If you want to get all toxins related the term, just click getSequence button and an entry list will display. (3,4,5) Filter and select manually can be done via a filter through keyword matches. (6) The selected sequences can be downloaded smoothly as Excel file and Fasta file by push the Excel download and Fasta download button respectively.

5) How can I extract toxins preferred basic on function, structure as well species information?
Thanks to the detailed classification system of TO and flexible query system, users can get toxins they are interested in accurately by browsing TO views and advance text search. A BLAST search engine is also available for sequence query.

6) How do I submit a suggestion or a new toxin to the database?
Any suggestions are welcome and can be submitted via Submission page or sent email to hqyone@hotmail.com or liangsp@hunnu.edu.cn. As to new entry register, we recommend that new sequence(s) should be submitted to a general database such as GenBank and SwissProt firstly and then inform us via the similar way as suggestion submission. As to small molecules or other type toxins, please email us directly. Detailed information about the author(s), taxon and function is required. We will check it and reply within four business days.

7) How can I download data from ATDB?
All data of ATDB toxin is available to public. User can download it via Download page.

8)What is the expected update cycle of the database.
The major update cycle of ATDB is two months, small revision is timely.

9) Why the database cannot work properly on my browsers?
The application has been developed in a Windows Internet Explorer context. Some differences of html protocols applied by various browsers may result in the problem. We have noticed the issue and will fix it in the update versions. In current status, we recommend you Internet Explorer 6.0 or laters and firefox browser.

11) What is the TO evidence codes?
Every annotation must be attributed to a source, which may be a literature reference, another database or a computational analysis. There are five TO evidence codes: