ATDB: a uni-database platform for animal toxins

Abstract

Venomous animals possess an arsenal of toxins for predation and defense. These toxins have great diversity in function and structure as well as evolution and therefore are of value in both basic and applied research. Recently, toxinomics researches using cDNA library sequencing and proteomics profiling have revealed a large number of new toxins. Although several previous groups have attempted to manage these data, most of them are restricted to certain taxonomic groups and/or lack effective systems for data query and access. In addition, the description of the function and the classification of toxins is rather inconsistent resulting in a barrier against exchanging and comparing the data. Here, we report the ATDB database and website which contains more than 3235 animal toxins from UniProtKB/Swiss-Prot and TrEMBL and related toxin databases as well as published literature. A new ontology (Toxin Ontology) was constructed to standardize the toxin annotations, which includes 745 distinct terms within four term spaces. Furthermore, more than 8423 TO terms have been manually assigned to 2132 toxins by trained biologists. Queries to the database can be conducted via a user-friendly web interface at http://protchem.hunnu.edu.cn/toxin.

Figure 1.

Schematic overview of the pipeline of data integration in ATDB. All sequence data were downloaded by December 2006. Signal peptide sequences were extracted by an in-house Perl script. Taking these sequences as probes, we searched the NCBI-RefSeq database by BLASTP and filtered by the key word ‘venom gland’ in tissue specificity annotations. Toxin ontology construction and annotation were mainly done manually by trained biologists.

Figure 2.

The top-level structure of Toxion Ontology. It contains four term spaces to handle different aspects of toxin functions. Detailed descriptions about it can be found in main text.

Figure 3.

The tree view of species. It includes a left tree and a right table. (1) Users can focus and expand the branches of the tree by clicking leaves (Serpents suborder in this figure) and detailed information about the taxonomic group will be shown in the right table. (2) If you want to get all toxins related to the term, just click the ‘getSequence’ button to display the toxin list. (3, 4 and 5) Users can select toxins manually and filter them by keywords via a filter. (6) The selected sequences can be downloaded smoothly as Excel file and FASTA file by clicking the ‘Excel download’ and ‘Fasta download’ buttons, respectively.