Xenbase: a Xenopus Model Organism Database

描述(由申请人提供)：对非洲爪哇胚胎的研究证明了诱导相互作用在驱动脊椎动物模式形成、细胞规格和形态发生方面的重要性。非洲爪哇中胚层的诱导和模式是所有脊椎动物系统中最被理解的发育级联，在某些层面上可以与强大的无脊椎动物遗传系统相媲美，如果蝇和线虫。随着发育生物学进入后基因组时代，非洲爪哇系统的丰富历史和无与伦比的实验可操作性将为我们理解基因在调节胚胎发育中的作用做出巨大贡献。 尽管已公布或可在公共数据库中获得大量数据，但目前还没有专门用于存储和链接非洲爪哇数据的模式生物数据库。目前有超过400,000个非洲爪哇EST，非洲爪哇基因组计划已经产生了超过16亿个碱基对，超过500套完整的基因表达模式，大约20,000种出版物和大量的解剖学和组织学数据。由于缺乏解剖本体和集成数据库，目前需要大量的工作来搜索所需的信息，并且关系分析，例如将EST与表达模式匹配，目前是不可能的。该项目将建立一个生物模型数据库，专门存储、注释和分析非洲爪哇和热带非洲爪哇的生物数据。Xenopus数据的标准命名法和受控词汇表的开发和应用将允许所有不同形式的信息相互关联，并极大地增强计算分析的能力。除了为非洲爪哇社区提供关键资源外，这个数据库还将允许非洲爪哇研究人员产生的丰富的基因功能数据被研究其他系统的人使用，特别是那些基因功能更难分析的系统。

DESCRIPTION (provided by applicant): Studies on the Xenopus embryo demonstrated the importance of inductive interactions that drive vertebrate pattern formation, cell specification and morphogenesis. The induction and patterning of the Xenopus mesoderm is the best understood developmental cascade in any vertebrate system and on some levels rivals those of the powerful invertebrate genetic systems such as Drosophila and C. elegans. As developmental biology moves into the post-genomic era the rich history and unparalleled experimental manipulability of the Xenopus system is poised to make enormous contributions to our understanding of the role genes play in regulating embryonic development. Despite the vast amount of data that has been published or is available in public databases, there is at present no model organism database dedicated to storing and interlinking Xenopus data. Over 400,000 Xenopus EST's are available, the Xenopus genome project has generated over 1.6 billion base pairs, over 500 whole mount sets of gene expression patterns are available, some 20,000 publications and an enormous amount of anatomical and histological data exists. Due to the lack of an anatomical ontology and an integrated database a vast amount of effort is currently required to search for required information and relational analysis, for example matching an EST to an expression pattern, is not currently possible. This project will implement a model organism database dedicated to storing, annotating and analyzing biological data on both Xenopus laevis and X. tropicalis. The development and application of standard nomenclatures and controlled vocabularies to Xenopus data will allow all of the different forms of information to be related to each other and vastly increase the power of computational analysis. In addition to providing a critical resource to the Xenopus community this database will also allow the wealth of data on gene function generated by Xenopus researchers to be used by those investigating other systems, especially those in which gene function is more difficult to analyze.