ATDB: a uni-database platform for animal toxins
Open Access
- 11 October 2007
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 36 (Database), D293-D297
- https://doi.org/10.1093/nar/gkm832
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 .Keywords
This publication has 14 references indexed in Scilit:
- Proteomic and peptidomic analysis of the venom from Chinese tarantula Chilobrachys jingzhaoProteomics, 2007
- Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebaseToxicon, 2005
- A novel strategy for the identification of toxinlike structures in spider venomProteins-Structure Function and Bioinformatics, 2005
- Australian funnel-web spiders: master insecticide chemistsToxicon, 2004
- Tarantulas: eight-legged pharmacists and combinatorial chemistsToxicon, 2004
- The wonderful world of spiders: preface to the special Toxicon issue on spider venomsToxicon, 2004
- The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003Nucleic Acids Research, 2003
- Mechanisms for Evolving Hypervariability: The Case of ConopeptidesMolecular Biology and Evolution, 2001
- Gene Ontology: tool for the unification of biologyNature Genetics, 2000
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994