Structured and graphical queries for Drosophila neuroscience data

神经系统疾病是英国国家医疗服务体系最大的一项支出，在发达国家，三分之一的人会在一生中的某个时候受到影响。设计治疗方法需要我们首先了解大脑是如何工作的，但它是已知的最复杂的器官，因此更简单的模型是必不可少的。果蝇的大脑为研究大脑功能提供了一个极好的模型系统。它比哺乳动物的大脑小几个数量级，也更简单，但在基因上却非常相似。此外，像哺乳动物的大脑一样，大脑具有学习的能力，并根据经验和环境背景进行重塑。对果蝇和其他昆虫的大脑的研究有很长的历史。这为现代研究果蝇大脑的构造和功能的遗传学基础奠定了坚实的基础。这类研究利用了一系列日益强大的基因技术，这些技术可以破坏特定的区域、细胞和基因，从而测量它们的功能。与此同时，越来越复杂的成像技术正在以越来越精细的细节揭示果蝇大脑的结构。正在收集的数据的巨大数量和微观细节给想要建立和传达大脑功能的连贯模型或共享他们用于实验的工具的研究人员带来了一个问题。在新信息的暴风雪中导航变得特别困难，因为名称多种多样，而且往往令人困惑，这是一个有着如此悠久历史的复杂领域的必然特征。我们的目标是通过建立一个基于网络的地图集和搜索工具--虚拟苍蝇大脑来解决这个问题。用户将能够通过点击大脑3D参考图像中的标记区域，或者通过搜索和浏览命名大脑区域和连接它们的脑细胞的结构化词汇来导航。用户将能够通过浏览和搜索从他们找到的词汇中选择词汇，从而突出显示不同颜色的大脑区域。选择一个术语还会提示显示与该术语相关的各种信息：其他图像的链接；引用它们所在科学论文的书面定义；帮助消除术语混淆或冲突用法的同义词和注释。用户将能够使用这些查询生成的术语列表来搜索存储在FlyBase中的相关数据，FlyBase是果蝇群落的主要遗传数据库。这将使他们能够找到在清单上的结构中表达的基因，或者那些已知参与这些结构的构造或功能的基因。它还将使他们能够搜索针对这些结构的复杂遗传试剂。最后，我们将提供工具，帮助新的研究人员和学生探索和了解大脑是如何组织的，并允许专家用户使用我们的结构化词汇和for来标记他们自己的数据。

Disorders of the nervous system account for the single biggest cost to the National Health Service and affect one in three people in the developed world at some point in their life. Designing treatment therapies requires us to understand first how the brain works yet it is the most complex organ known and thus simpler models are essential. The brain of the fruit fly, Drosophila melanogaster, provides an excellent model system for studying how brains function. It is orders of magnitude smaller and simpler than a mammalian brain, yet genetically it is remarkably similar. Moreover, like mammalian brains, is capable of learning and is remodelled in response to experience and environmental context. There is a large history of research into the brain of Drosophila and other insects. This gives a firm foundation to modern studies of the genetic basis of how the Drosophila brain is built and functions. Such studies take advantage of an increasingly powerful array of genetic techniques that allow specific regions, cells and genes to be disrupted thus measuring their function. At the same time, increasingly sophisticated imaging techniques are revealing the structure of the Drosophila brain in ever-finer detail. The sheer volume and microscopic detail of the data being collected poses a problem to researchers wanting to build and communicate coherent models of brain function or to share the tools they use for their experiments. Navigating through the blizzard of new information is made particularly difficult by the varying and often confusing nomenclature that is an inevitable feature of a complicated field with such a long history. We aim to remedy this by building a web-based atlas and search tool - Virtual Fly Brain. Users will be able to navigate by clicking on labelled regions in a 3D reference image of a brain, or by searching and browsing a structured vocabulary which names brain regions and the brain cells which connect them. Users will be able to highlight brain regions in various colours by choosing terms in the vocabulary they find through browsing and searching. Choosing a term will also prompt the display of various information related to that term: links to additional images; written definitions with references to the scientific papers they come from; synonyms and comments to help disambiguate confusing or conflicting usage of terms. Users will be able to use the lists of terms generated by these queries to search for related data stored in FlyBase, the main genetic database of the Drosophila community. This will allow them to find genes expressed in structures on the list or which are known to be involved in the construction or function of these structures. It will also allow them to search for sophisticated genetic reagents which target these structures. Finally, we will provide tools to help new researchers and students to explore and learn how the brain is organised and allow expert users to label their own data using our structured vocabulary and for.