THE FLYDATA PROJECT: Decision Support and Semantic Organization of Laboratory Data in Drosophila Gene Expression Experiments (Revised)

在生物学中，图像越来越重要。显微镜技术的进步现在使我们能够看到单个基因在组织中的活动时间和地点。在牛津，我们正在进行实验，研究果蝇睾丸中一千多个基因的表达，果蝇是基因组序列已经确定的“模式”生物之一，目的是发现它们在精子形成中的作用。为此，我们使用了一种称为原位杂交的技术，该技术允许我们对每个选定基因沿精子分化途径表达的位置进行成像。当它们可用时，我们的结果将在一个可公开访问的数据库中发表，即果蝇基因表达数据库，以便其他人可以使用它们。由于这些基因中的许多与人类相似，因此这项工作可能对男性不育症的临床治疗具有重要意义。因为我们希望研究对正常精子形成至关重要的基因，我们首先测量了大约14000个果蝇基因在精子发育异常的突变株中的表达改变程度，并将这些数据与果蝇遗传信息公共数据库FlyBase的在线信息联系起来。只有这样，我们才能比较所有这些基因的特性，并将它们归类为功能类，从中选择有代表性的个体进行原位成像。毫不奇怪，我们发现不可能一次记住所有这些信息，这使得做出这些决定变得困难。光是记录所有的信息就是一项复杂而耗时的任务。FlyData计划的目的是开发一个简单但功能强大的电脑资讯管理及决策支援系统，以协助我们(a)以有意义的方式整理果蝇基因表达实验所得的所有实验室数据，(b)将这些数据与网上资讯联系起来，以及(c)透过一套精心设计的图形使用者介面，透过标准网页浏览器，获得对这个多维资讯空间的不同看法。给我们一个基因或一组基因的正确信息组合，我们需要这些信息来支持我们的决策过程。因此，FlyData系统将帮助我们浏览面对的大量数据。此外，它将记录我们的研究决策，谁做出了这些决策，何时以及为什么做出这些决策，从而创建了我们研究“旅程”的完整记录。通过使我们能够对原始数据进行注释，它既可以帮助我们随后撰写报告和科学论文，也可以使我们能够将我们的结果自动发布到果蝇基因表达数据库。由于生物学家和计算机科学家之间密切的跨学科合作，我们开发的FlyData系统将完全满足我们的研究需求。它将使用开放标准以计算机可处理的形式输出原始科学观察和描述性注释，为与全球其他信息管理系统交换提供基础。我们将使用免费的、轻量级的软件工具和敏捷的软件开发方法来构建和测试该系统，该系统将集中于即时需求，但易于适应处理不断变化的需求，例如需要包含额外类型的信息。我们希望，在进一步的支持下，我们将能够将FlyData系统增强为一个通用的、社区支持的实验室信息管理和决策支持系统，用于生物显微镜研究。

In biology, images are increasingly important. Advances in microscopy now allow us to see when and where individual genes are active in tissues. In Oxford, we are undertaking experiments to investigate the expression of more than a thousand genes in the testis of the fruit fly Drosophila, one of the 'model' organisms whose genome sequence has been determined, in order to discover their role in sperm formation. For this we use a technique known as in situ hybridization, that permits us to image the location at which each selected gene is expressed along the sperm differentiation pathway. As they become available, our results will be published in a publicly accessible database, the Drosophila Testis Gene Expression Database, so others can use them. Because many of these genes are similar to those in humans, such work could have importance for the clinical treatment of male infertility. Because we wish to study genes critical for normal sperm formation, we first measure the degree to which expression of each of the ~14,000 Drosophila genes is altered in mutant fly strains with abnormal sperm development, and relate these data with on-line information from FlyBase, a public database of genetic information about Drosophila. Only then can we compare the properties of all these genes and group them into functional classes from which to select representative individuals for in situ imaging. Not surprisingly, we find it impossible to hold all this information in our heads at one time, making these decisions difficult. Just keeping track of all the information is a complex and time-consuming task. The purpose of the FlyData Project is to develop a simple but powerful computer-based information management and decision support system that will help us (a) to organise all the laboratory data arising from our Drosophila gene expression experiments in meaningful ways, (b) to relate them to on-line information, and (c) to obtain different views into this multi-dimensional information space using a standard web browser, by means of a set of carefully-designed graphical user interfaces, giving us just the right combinations of information about one gene, or a group of genes, that we need to support our decision-making processes. The FlyData system will thus help us navigate the mass of data that confronts us. Further, it will record our research decisions, who made them, and when and why they were made, thus creating a complete record of our research 'journey'. By enabling us to annotate the raw data, it will both assist our subsequent writing of reports and scientific papers, and will also enable us to automate the publication of our results to the Drosophila Testis Gene Expression Database. As a consequence of the close interdisciplinary collaboration between biologists and computer scientists, the FlyData system we develop will exactly meet our research needs. It will use open standards to export original scientific observations and descriptive annotations in a computer-processable form, providing a foundation for exchange with other information management systems worldwide. We will use freely available, lightweight software tools and agile software development methods to build and test this system, which will be focused on immediate needs yet readily adapted to handle evolving requirements, such as the need to include an additional type of information. We hope that, with further support, we will be able to enhance the FlyData system into a general-purpose, community-supported laboratory information management and decision support system for biological microscopy research.