Mattingly Carolyn J, Rosenstein Michael C, Davis Allan Peter, Colby Glenn T, Forrest John N, Boyer James L
Department of Bioinformatics, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672, USA.
Toxicol Sci. 2006 Aug;92(2):587-95. doi: 10.1093/toxsci/kfl008. Epub 2006 May 4.
Chemicals in the environment play a critical role in the etiology of many human diseases. Despite their prevalence, the molecular mechanisms of action and the effects of chemicals on susceptibility to disease are not well understood. To promote understanding of these mechanisms, the Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org/) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. CTD integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. These comparisons will facilitate understanding of structure-function correlations and the genetic basis of susceptibility. Manual curation and integration of cross-species chemical-gene and chemical-protein interactions from the literature are now underway. These data will provide information for building complex interaction networks. New CTD features include (1) cross-species gene, rather than sequence, query and visualization capabilities; (2) integrated cross-links to microarray data from chemicals, genes, and sequences in CTD; (3) a reference set related to chemical-gene and protein interactions identified by an information retrieval system; and (4) a "Chemicals in the News" initiative that provides links from CTD chemicals to environmental health articles from the popular press. Here we describe these new features and our novel cross-species curation of chemical-gene and chemical-protein interactions.
环境中的化学物质在许多人类疾病的病因学中起着关键作用。尽管它们普遍存在，但化学物质的分子作用机制以及对疾病易感性的影响仍未得到充分理解。为了促进对这些机制的理解，比较毒理基因组学数据库（CTD；http://ctd.mdibl.org/）提供了关于化学物质、相关基因和蛋白质及其在脊椎动物和无脊椎动物中相互作用的经过科学审查和整理的信息。CTD整合了序列、参考文献、物种、微阵列和一般毒理学信息，为毒理基因组学研究提供了一个独特的集中资源。该数据库还提供可视化功能，能够对基因和蛋白质序列进行跨物种比较。这些比较将有助于理解结构 - 功能相关性以及易感性的遗传基础。目前正在对文献中的跨物种化学物质 - 基因和化学物质 - 蛋白质相互作用进行人工整理和整合。这些数据将为构建复杂的相互作用网络提供信息。CTD的新功能包括：（1）跨物种基因而非序列的查询和可视化功能；（2）与CTD中化学物质、基因和序列的微阵列数据的集成交叉链接；（3）与通过信息检索系统识别的化学物质 - 基因和蛋白质相互作用相关的参考集；（4）“新闻中的化学物质”倡议，该倡议提供从CTD化学物质到大众媒体环境健康文章的链接。在这里，我们描述这些新功能以及我们对化学物质 - 基因和化学物质 - 蛋白质相互作用的新型跨物种整理。
