Extending InterMine to yeast rat and zebrafish model organism databases

描述（由申请人提供）：对模式生物进行实验是生物医学研究的基础。其中最重要的三项是芽殖酵母（基础研究）、大鼠（药理学、行为学和神经学研究）和斑马鱼（发育、神经学和毒理学研究）。已经建立了用于捕获和管理关于这些模式生物的丰富数据的数据库，并且统称为模式生物数据库（MOD）。现代生物学已经产生了人类以及这些模式生物的完整DNA序列（“基因组”）。反过来，这导致了一个新的研究时代，在这个时代，实验是在整个基因组规模进行的。基因组学的成功引发了一个挑战，即在MOD中整合基因组数据集，使所有科学家都可以灵活地查询和提取数据;而不仅仅是被称为生物信息学家的专家，尽管为生物信息学家提供强大的工具也很重要。作为先前支持另一种模式生物果蝇的工作的一部分，InterMine软件的开发大大提高了科学家利用基因组数据的能力和灵活性。InterMine被设计成易于应用于生物学和有机体的其他领域。事实上，它目前正被用于管理来自NIH资助的modENCODE项目的数据，该项目正在实验性地表征果蝇和线虫模式生物的整个基因组。本项目的目的是将InterMine软件应用于三种MOD：芽殖酵母，大鼠和斑马鱼。这为每个数据库提供了许多优点：用户社区需要但尚未提供的功能; MOD之间的标准接口和一组功能;不同MOD之间相互操作的机会，提供了一种工具来比较和对比这组生物体之间的基因和蛋白质的行为，这是一种目前通常不可用的功能。该项目将由位于英国剑桥的InterMine开发团队与位于斯坦福大学（酵母，SGD）、威斯康星州医学院（大鼠，RGD）和俄勒冈州大学（斑马鱼，ZFIN）的三个MOD开发和维护团队合作开展。这一提议为每个地点提供一名工作人员，由此产生的小组将共同努力，将数据输入InterMine数据库，并为其增加分析工具，这些数据库将在国防部每个地点和用户界面中加以整合。以这种方式共同努力的一个好处是，一个地点的发展可以立即使其他地点受益。到项目结束时，国防部将能够为其研究界提供更大的功能，对InterMine基础软件的改进将免费提供给更广泛的社区。拟议的项目是独特的，在其整合的实验结果在主要模式生物。这种整合对于我们深入了解分子遗传学，细胞生物学，发育生物学，生理学以及最重要的人类健康和疾病至关重要。公共卫生相关性：最近人类基因组序列的解码通过改善对人类发育、功能、衰老和疾病的理解，对人类医疗保健的未来产生了前所未有的影响。然而，为了充分理解这些事件而必须进行的许多实验工作无法在人类中进行，因此必须在所谓的模式生物中进行。拟议项目将解决迫切需要提高效率的问题，以便能够整合、分析和比较正在生成的大量模式生物数据，从而提高对人类的了解，从而更好地进行疾病诊断、预后、预防和治疗。

DESCRIPTION (provided by applicant): Conducting experiments on model organisms is fundamental to biomedical research. Three of the most important are budding yeast (fundamental studies), rat (pharmacological, behavioral and neurological studies) and zebrafish (developmental, neurological and toxicological studies). Databases to capture and curate the wealth of data on these model organisms have been established and are known collectively as Model Organism Databases (MODs). Modern biology has resulted in the complete DNA sequence (`genome') of the human as well as these model organisms. In turn this has led to a new era of research in which experiments are carried out at the whole genome scale. The success of genomics has fuelled a challenge to integrate genomic datasets within the MODs in such a way that querying them and extracting data in a flexible fashion is possible for all scientists; not just specialists known as bioinformaticians, although it is also important to provide bioinformaticians with powerful tools. As part of previous work in support of another model organism, the fruitfly, InterMine software was developed to greatly increase the power and flexibility with which scientists can utilize genomic data. InterMine was designed to be applied easily to other areas of biology and organisms. Indeed it is currently being used to manage data from the NIH-funded modENCODE project which is experimentally characterizing the entire genomes of the fruitfly and nematode model organisms. The aim of this project is to apply the InterMine software to three MODs: budding yeast, rat and zebrafish. This provides a number of advantages to each database: functionality that their user communities demand but that are not yet available; a standard interface and set of functionality between MODs; an opportunity for the different MODs to inter-operate providing a tool to compare and contrast the behavior of genes and proteins between this set of organisms, a feature that is not generally available today. This project will be carried out as a collaboration between the team that developed InterMine, based in Cambridge UK, and the teams that develop and maintain the three MODs, based at Stanford University (yeast, SGD), the Medical College of Wisconsin (rat, RGD) and the University of Oregon (zebrafish, ZFIN). This proposal provides one staff member per site, and the resulting team will work together to transfer data into, and add analysis tools to, InterMine databases that will be integrated at each MOD site and within their user interfaces. A benefit of working together in this way is that developments at one site can immediately benefit the others. By the end of the project the MODs will be able to provide far greater functionality to their research communities, and improvements to the underpinning InterMine software will be freely available to the broader community. The proposed project is unique in its integration of experimental results across the major model organisms. This integration is essential for our advanced understanding of molecular genetics, cell biology, developmental biology, physiology, and most importantly, human health and disease. PUBLIC HEALTH RELEVANCE: The recent decoding of the human genome sequence has unprecedented implications for the future of human healthcare through improved understanding of human development, functioning, aging and disease. However, much of the experimental work that has to be done to fully understand these events cannot be done in humans and must therefore be carried out in so-called model organisms. The proposed project will address a pressing need to improve the efficiency with which the huge amounts of Model Organism data being generated can be integrated, analysed and compared, which will lead to improved understanding of humans and thus to better disease diagnosis, prognosis, prevention and cure.