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

• 批准号: BB/G02247X/1
• 负责人: James Armstrong
• 金额: $ 37.23万
• 依托单位: University of Edinburgh
• 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%2FG02247X%2F1
• 关键词: Structured; graphical; queries; Drosophila; neuroscience

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.

神经系统疾病是国民健康服务体系的最大单一成本，在发达国家，每三个人中就有一个人在一生中的某个时候受到神经系统疾病的影响。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很好的模型系统。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。这为现代研究果蝇大脑的构建和功能的遗传基础奠定了坚实的基础。这些研究利用了一系列日益强大的遗传技术，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更精细的细节揭示果蝇大脑的结构。所收集数据的庞大数量和微观细节给那些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，因为术语变化不定，而且往往令人困惑，这是一个具有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-虚拟苍蝇大脑来弥补这一点。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表进行导航。用户将能够通过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。选择一个术语还将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，参考它们来自的科学论文;同义词和注释，以帮助消除术语的混淆或冲突用法。用户将能够使用由这些查询生成的术语列表来搜索存储在果蝇群体的主要遗传数据库FlyBase中的相关数据。这将使他们能够找到在列表上的结构中表达的基因，或者已知参与这些结构的构建或功能的基因。这也将使他们能够寻找针对这些结构的复杂基因试剂。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标记自己的数据。

项目成果

Building the central complex in Drosophila: the generation and development of distinct neural subsets.

构建果蝇的中央复合体：不同神经亚群的产生和发展。

• DOI: 10.1002/cne.22285
• 发表时间: 2010
• 期刊: The Journal of comparative neurology
• 作者: Young JM

Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library.

• DOI: 10.1242/dev.111054
• 发表时间: 2014-10
• 期刊: Development (Cambridge, England)
• 作者: Lowe N;Rees JS;Roote J;Ryder E;Armean IM;Johnson G;Drummond E;Spriggs H;Drummond J;Magbanua JP;Naylor H;Sanson B;Bastock R;Huelsmann S;Trovisco V;Landgraf M;Knowles-Barley S;Armstrong JD;White-Cooper H;Hansen C;Phillips RG;UK Drosophila Protein Trap Screening Consortium;Lilley KS;Russell S;St Johnston D
• 通讯作者: St Johnston D

BrainTrap: a database of 3D protein expression patterns in the Drosophila brain.

• DOI: 10.1093/database/baq005
• 发表时间: 2010-07-06
• 期刊: Database : the journal of biological databases and curation
• 作者: Knowles-Barley S;Longair M;Armstrong JD
• 通讯作者: Armstrong JD

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
• 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