Wormbase ParaSite

寄生虫（蠕虫）造成巨大的经济负担，英国每年的农业损失超过1亿英镑。在地球仪范围内，蠕虫也是导致人类长期慢性疾病的原因。英国在针对蠕虫的研发方面处于领先地位，尽管与感染的影响相比，全球投资不成比例地低。蠕虫是多种多样的-这个术语包括蛔虫和扁虫-没有一个单一的模式物种可以捕捉到所涉及的致病机制的范围。因此，研究人员天生对物种之间的比较感兴趣。现在已经公布了30多个物种的基因组，还有更多的物种可以利用。除了它们的基因组，还产生了大规模的功能基因组学数据集，描述了10多个物种的关键生命周期转变。为了推动蠕虫研究进入基因组时代，我们于2014年建立了WormBase ParaSite。该资源现在包含100多个蠕虫基因组草案。基因和基因组可以被探索，使更多的了解蠕虫生物学，以加快发展新的战略蠕虫控制。在其头两年，有8个公共发布的资源，并在2015年该网站被访问了29000独立用户。除了访问基因结构和基因组草案的功能注释外，用户还能够检查基因之间的进化关系，并寻找物种之间的差异和相似之处，这些差异和相似之处可能是蠕虫生物学差异和相似之处的基础。该资源为浏览和搜索提供了快速直观的界面，并包含一个用于提取自定义数据集的界面。已经组织了几次讲习班，提供使用培训，这项建议将为WormBase ParaSite的维护和改进提供资金。我们打算将所有公开的线虫和扁虫基因组组装，因为他们成为可用的。由于测序技术的变化，研究小组将产生新的和更好的现有基因序列的版本。然而，这些序列在许多情况下不会被注释，因此我们将提供一种自动化的方式来注释具有一致基因结构和功能描述的裸基因组。基因家族的定义仍将是一项至关重要的活动。然而，我们将提高进化历史可以推断的速度，准确性和可扩展性。我们还将大大改进将基因表达或基因组变异的大规模研究数据纳入资源的方式。特别是，一个新的基因表达图谱将包括基因表达数据的互动探索。为了帮助确定新的药物靶标或确定现有药物的重复使用可能性，WormBase ParaSite将包括靶标和化学数据的链接（通过链接到ChEMBL数据库）。我们还将使用户能够查询可用的表型数据。除了新的功能，我们将经常更新网站，以提供快速访问新数据。我们将继续提供有关如何使用该资源的培训，并维持一个实时和反应迅速的求助台。

Parasitic worms (helminths) cause a massive economic burden, with agricultural losses in the UK exceeding £100 million per annum. Across the globe helminths are also responsible for long term, chronic diseases in humans. The UK is a leader in research and development targeting helminths, despite global investment being disproportionately low compared with the impact of infections. Helminth are diverse - the term covers both round worms and flatworms - and no single model species can capture the range of disease-causing mechanisms involved. Researchers are therefore inherently interested in making comparisons between species. The genomes of more than 30 species are now published and many more available. Alongside their genomes, large scale functional genomics datasets have been produced describing key life cycle transitions for more than 10 species. To drive helminth research into the genomic era, we established WormBase ParaSite in 2014. The resource now contains more than 100 draft genomes of helminths. Genes and genomes can be explored, enabling a greater understanding of helminth biology to accelerate the development of new strategies for helminth control.In its first two years, there have been 8 public releases of the resource and in 2015 the website was accessed by 29000 unique users. In addition to accessing gene structures and functional annotation for draft genomes, users are able to examine evolutionary relationships between genes and look for the differences and similarities between species that may underpin differences and similarities in helminth biology. The resource provides fast and intuitive interfaces for browsing and searching and contains an interface for extracting custom datasets. Several workshops have been organised to provide training in its use.This proposal will fund the maintenance and improvement of WormBase ParaSite. We intend to incorporate all publicly available nematode and flatworm genome assemblies as they become available. Due to changes in sequencing technology, research groups will produce new and better versions of existing gene sequences. However, these sequences will in many cases not be annotated, so we will provide an automated way to annotate naked genomes with consistent gene structures and functional descriptions. Defining gene families will remain a critically important activity. However, we will increase the speed, accuracy and scalability in which evolutionary histories can be inferred. We will also greatly improve the way in which data from large-scale studies on gene expression or genome variation are included into the resource. In particular, a new Gene Expression Atlas will be included for interactive exploration of gene expression data. To help identify new drug targets or to identify re-use possibilities for existing drugs, WormBase ParaSite will include links to targets and chemistry data (by linking to the ChEMBL database). We will also enable users to query available phenotypic data.In addition to the new features, we will frequently update the site to provide rapid access to new data. We will continue to provide training on the use of the resource and maintain a live and responsive helpdesk.