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ATDB: a uni-database platform for animal toxins
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 profil...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238984/ https://www.ncbi.nlm.nih.gov/pubmed/17933766 http://dx.doi.org/10.1093/nar/gkm832 |
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author | He, Quan-Yuan He, Quan-Ze Deng, Xing-Can Yao, Lei Meng, Er Liu, Zhong-Hua Liang, Song-Ping |
author_facet | He, Quan-Yuan He, Quan-Ze Deng, Xing-Can Yao, Lei Meng, Er Liu, Zhong-Hua Liang, Song-Ping |
author_sort | He, Quan-Yuan |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2238984 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-22389842008-02-12 ATDB: a uni-database platform for animal toxins He, Quan-Yuan He, Quan-Ze Deng, Xing-Can Yao, Lei Meng, Er Liu, Zhong-Hua Liang, Song-Ping Nucleic Acids Res Articles 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. Oxford University Press 2008-01 2007-10-11 /pmc/articles/PMC2238984/ /pubmed/17933766 http://dx.doi.org/10.1093/nar/gkm832 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles He, Quan-Yuan He, Quan-Ze Deng, Xing-Can Yao, Lei Meng, Er Liu, Zhong-Hua Liang, Song-Ping ATDB: a uni-database platform for animal toxins |
title | ATDB: a uni-database platform for animal toxins |
title_full | ATDB: a uni-database platform for animal toxins |
title_fullStr | ATDB: a uni-database platform for animal toxins |
title_full_unstemmed | ATDB: a uni-database platform for animal toxins |
title_short | ATDB: a uni-database platform for animal toxins |
title_sort | atdb: a uni-database platform for animal toxins |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238984/ https://www.ncbi.nlm.nih.gov/pubmed/17933766 http://dx.doi.org/10.1093/nar/gkm832 |
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