Structured and graphical queries for Drosophila neuroscience data

神经系统疾病是英国国民健康服务体系（National Health Service）最大的单项支出，在发达国家有三分之一的人在一生中的某个阶段受到影响。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（Drosophila melanogaster）的大脑为研究大脑的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，也简单几个数量级，但在基因上却惊人地相似。此外，像哺乳动物的大脑一样，能够学习，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进行了大量的研究。这为果蝇大脑构造和功能的遗传基础的现代研究奠定了坚实的基础。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以越来越精细的细节揭示果蝇大脑的结构。对于想要建立和交流连贯的大脑功能模型或分享他们用于实验的工具的研究人员来说，所收集的数据的绝对数量和微观细节给他们带来了一个问题。对于一个有着如此悠久历史的复杂领域来说，多变且常常令人困惑的命名法是一个不可避免的特征，这使得在海量新信息中导航变得尤为困难。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来弥补这一点——虚拟苍蝇大脑。用户可以通过点击大脑3D参考图像中的标记区域，或者通过搜索和浏览一个结构化的词汇表来导航，该词汇表列出了大脑区域和连接这些区域的脑细胞的名称。用户可以通过在浏览和搜索中找到的词汇中选择词汇，用不同的颜色突出显示大脑区域。选择一个术语还会提示显示与该术语相关的各种信息：链接到其他图像；书面定义，并注明其来源的科学论文；同义词和注释，以帮助消除歧义混淆或冲突的使用术语。用户将能够使用这些查询生成的术语列表来搜索存储在果蝇社区主要遗传数据库FlyBase中的相关数据。这将使他们能够找到在清单上的结构中表达的基因，或者已知与这些结构的构建或功能有关的基因。这也将使他们能够寻找针对这些结构的复杂遗传试剂。最后，我们将提供工具来帮助新的研究人员和学生探索和学习大脑是如何组织的，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.