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Structured and graphical queries for Drosophila neuroscience data

果蝇神经科学数据的结构化和图形查询

基本信息

批准号：
BB/G02233X/1
负责人：
Cahir O'Kane
金额：
$ 43.77万
依托单位：
University of Cambridge
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2009
资助国家：
英国
起止时间：
2009 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FG02233X%2F1
关键词：
Structured graphical queries Drosophila neuroscience

项目摘要

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.

神经系统疾病是国家卫生服务的最大成本，在发达国家，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，它能够学习并根据经验和环境背景进行重塑。对果蝇和其他昆虫大脑的研究有着悠久的历史。这为果蝇大脑的构建和功能的遗传基础的现代研究奠定了坚实的基础。此类研究利用了一系列日益强大的遗传技术，可以破坏特定区域、细胞和基因，从而测量它们的功能。与此同时，日益复杂的成像技术正在更详细地揭示果蝇大脑的结构。所收集的数据的庞大数量和微观细节给想要建立和交流大脑功能的连贯模型或共享他们在实验中使用的工具的研究人员带来了问题。由于术语多种多样且常常令人困惑，因此在新信息的暴风雨中导航变得特别困难，这是一个历史悠久的复杂领域不可避免的特征。我们的目标是通过构建一个基于网络的图集和搜索工具——Virtual Fly Brain 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进行导航，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。用户将能够通过在浏览和搜索找到的词汇中选择术语，以各种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：其他图像的链接；书面定义并参考其来源的科学论文；同义词和注释可帮助消除术语的混乱或冲突用法。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（果蝇社区的主要遗传数据库）中的相关数据。这将使他们能够找到列表中结构中表达的基因或已知参与这些结构的构建或功能的基因。它还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来标记自己的数据。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Geppetto: a reusable modular open platform for exploring neuroscience data and models.

DOI：
10.1098/rstb.2017.0380
发表时间：
2018-09-10
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
0
作者：
Cantarelli M;Marin B;Quintana A;Earnshaw M;Court R;Gleeson P;Dura-Bernal S;Silver RA;Idili G
通讯作者：
Idili G

The Drosophila anatomy ontology.