Wormbase-ParaSite

扁虫和蛔虫是多种多样的生物，其中包括导致严重的人类、兽医和植物疾病的生物。它们的全球影响难以衡量，但据估计，每年的人类发病率至少相当于5000万年的生产寿命（如艾滋病毒/艾滋病为8500万年），植物寄生线虫造成的农业损失可以用数亿美元来衡量。尽管它们对人类健康有影响，但最近的一份报告强调指出，寄生蠕虫每年仅吸引7700万美元的研究支出（比较艾滋病毒/艾滋病的11亿美元）。由于在不同宿主物种中引起的病理范围很广，没有一个单一的模式物种可以捕获所涉及的致病机制的范围。因此，寄生虫学家天生就对在许多不同物种之间进行比较感兴趣。获得基因组规模的数据集已经彻底改变了原生动物病原体的分子和细胞生物学研究，推进了基础和应用研究，但这只是现在才开始发生在寄生虫上。主要的测序计划正在进行中，大规模的功能基因组学数据集开始出现（例如RNA-Seq正变得普遍）。研究多个分离株的基因组变异，以解决临床、流行病学或应用农业问题，显然是下一步的工作。虽然新的基因组规模数据集的出现非常令人兴奋，但与现有的参考基因组相比，基因组通常处于相对较差的组装和注释状态。此外，组织基因组信息的主流范式（本质上是基因组浏览器和支持它的底层数据模型）相对不适合探索数百个高度碎片化的基因组，这些基因组具有有限的功能特征。在这个应用中，我们建议创建一个新的资源来组织、分类和探索数百个蠕虫基因组，促进基于序列的数据的利用，以理解和最终控制蠕虫诱导的病理。提议的资源将被称为WormBase- parasite，并将与WormBase（模型线虫秀丽隐杆线虫的主要资源）战略性地保持一致。具体而言，该资源将提供：(a)未注释的蠕虫基因组的基因结构和功能注释。(b)比较基因组分析、可视化和查询。(c)通过研究科学家可以使用的直观查询建立界面探索和挖掘完整数据集的方法。(d)在其他注释背景下实现高通量测序实验结果可视化的平台，从而实现功能基因组学和变异研究。(e)用于接受和整合蠕虫研究社区提交的功能性注释的基础设施。该项目将补充WormBase的现有范围（并利用现有内容），该项目为研究秀丽隐杆线虫模型的生物学家提供了宝贵的信息资源，因为该物种的基因组是最早被破译的物种之一。它将为处理大量增加的基因组提供额外的能力和工具，并明确侧重于与寄生虫学家最相关的信息。该资源还将提供来自扁虫（如吸虫和绦虫）的数据，这些数据不在WormBase的范围内。

Flatworms and roundworms are diverse groups of organisms and include those responsible for serious human, veterinary and plant diseases. Their global impact is hard to measure but annual human morbidity is estimated to be equivalent to at least 50 million productive years of life (c.f. 85M for HIV/AIDS), and agricultural losses from plant parasitic nematodes can be measured in hundreds of millions of dollars. Despite their impact on human health, a recent report highlighted that parasitic helminths attract only $77M per annum in research expenditure (cf. $1.1billion for HIV/AIDS). Due to the wide range of pathology caused in various host species, no single model species can capture the range of disease-causing mechanisms involved. Parasitologists are therefore inherently interested in making comparisons between many different species. Access to genomic-scale datasets has revolutionized molecular and cell biological studies of protozoan pathogens, advancing basic and applied research, but this is only now starting to happen for parasitic worms. Major sequencing programmes are now underway and large scale functional genomics datasets are beginning to emerge (e.g. RNA-Seq is becoming commonplace). Studies of genomic variation in multiple isolates, to address clinical, epidemiological or applied agricultural questions, are the obvious next steps. While the emergence of new genome-scale datasets is immensely exciting, genomes are often produced in a relatively poor states of assembly and annotation compared to existing reference genomes. Moreover, the prevailing paradigm for organising genomic information (essentially, the genome browser and the underlying data models that support this) are relatively poorly fitted to the exploration of hundreds of highly fragmented genomes with limited functional characterisation. In this application, we propose the creation of a new resource to organise, classify and allow the exploration hundreds of worm genomes, facilitating the exploitation of sequence-based data for understanding and ultimately controlling worm-induced pathology.The propose resource will be called WormBase-ParaSite, and will be strategically aligned with WormBase (the main resource for the model nematode Caenorhadbitis elegans). Specifically the resource will provide: (a) Gene structures and functional annotation for unannotated worm genomes. (b) Comparative genomic analysis, visualisation and querying. (c) Methods for exploration and data mining the complete data set, through an intuitive query-building interface accessible to research scientists. (d) A platform for the visualisation of the results of high-throughput sequencing experiments in the context of other annotation that enables functional genomics and variation studies. (e) An infrastructure for accepting and integrating functional annotation submitted from the community engaged in worm research.The project will complement the existing scope (and leverage the existing content) of WormBase, which has supplied biologists working on the model worm Caenorhabditis elegans with an invaluable information resource since the genome of this species was one of the first to be deciphered. It will provide additional capacity and tools for the handling of a massively increased quantity of genomes, with a clear focus on the information that is most relevant to parasitologists. The resource will also provide a home for data from the flatworms, such as flukes and tapeworms, which are outside the scope of WormBase.