InterMOD: integrated data and tools to support model organism research

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，并支持导致医疗保健进步的研究。五个最重要的模型是小鼠（发育和行为研究）、线虫（发育和寄生虫学研究）、芽殖酵母（基础分子研究）、大鼠（药理学、行为和神经学研究）和斑马鱼（发育、神经学和毒理学研究）。模式生物数据库（MODs）已经建立，它可以捕获和管理这些模式生物的丰富数据。现代生物学已经产生了人类和这些模式生物的完整DNA序列（“基因组”）。反过来，这又导致了一个新的研究时代，在这个时代中，实验是在全基因组规模上进行的。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，以便所有科学家以及专业生物信息学家都可以以一种灵活的方式查询和提取数据。作为支持另一种模式生物果蝇的先前工作的一部分，以及最近管理来自美国国立卫生研究院资助的多机构modENCODE项目的数据，InterMine软件的开发大大增加了科学家利用基因组数据的能力和灵活性。InterMine被设计成可以很容易地应用于生物学和有机体的其他领域。本项目的目的是将InterMine软件应用于上述五种MODs：小鼠、线虫、芽殖酵母、大鼠和斑马鱼。这为每个数据库提供了许多优势：用户社区驱动的功能尚未可用；所有mod通用的标准接口；mod之间更大的互操作，以提供一套通用的工具来比较和对比这组生物中的基因和蛋白质的特性，这是目前普遍不具备的功能。该项目将由位于英国剑桥的InterMine开发团队和位于杰克逊实验室（小鼠，MGI）、安大略省癌症研究所（线虫，WormBase）、斯坦福大学（酵母，SGD）、威斯康星医学院（大鼠，RGD）和俄勒冈大学（斑马鱼，ZFIN）的开发和维护五种MODs的团队合作进行。该建议为每个站点提供一名工作人员，结果团队将一起工作，将数据传输到InterMine数据库，并添加分析工具，该数据库将集成到每个MOD站点。以这种方式合作的一个好处是，一个站点的开发可以立即使其他站点受益。到项目结束时，mod将能够为他们的研究社区提供更大的功能，并且对基础InterMine软件的改进将免费提供给更广泛的生物数据库社区。该计划的独特之处在于它整合了主要模式生物的实验结果。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。

DESCRIPTION (provided by applicant): Conducting experiments on model organisms is fundamental to biomedical research and underpins research that leads to healthcare advances. Five of the most important models are Mouse (developmental and behavioural studies), nematode (developmental and parasitological studies), budding yeast (fundamental molecular studies), rat (pharmacological, behavioural and neurological studies) and zebrafish (developmental, neurological and toxicological studies). Model Organism Databases (MODs), which capture and curate the wealth of data on these model organisms, have been established. 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 as well as specialist bioinformaticians. As part of previous work in support of another model organism, the fruitfly, and more recently to manage the data from the multi-institutional NIH-funded modENCODE project, 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. The aim of this project is to apply the InterMine software to the above five MODs: mouse, nematode, budding yeast, rat and zebrafish. This provides a number of advantages to each database: user-community driven functionalities that are not yet available; a standard interface common to all MODs; greater inter-operation between MODs to provide a common set of tools to compare and contrast the properties of genes and proteins within 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 five MODs, based at the Jackson Laboratory (mouse, MGI), the Ontario Institute for Cancer Research (nematode, WormBase), 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. 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 biological database 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.