InterMOD: integrated data and tools to support model organism research

描述(由申请人提供)：在模型生物上进行实验是生物医学研究的基础，也是导致医疗保健进步的研究的基础。五个最重要的模型是老鼠(发育和行为研究)、线虫(发育和寄生虫学研究)、发芽酵母(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)。已经建立了模式生物数据库(MODS)，该数据库捕捉和管理关于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，在整个基因组范围内进行实验。基因组学的成功引发了一项挑战，即如何将基因组数据集整合到MODS中，以便所有科学家以及专业生物信息学家都可以灵活地查询和提取数据。作为之前支持另一种模式生物--果蝇的工作的一部分，以及最近管理由美国国立卫生研究院资助的多机构modENCODE项目的数据的工作的一部分，Intermine软件被开发出来，以极大地提高科学家利用基因组数据的能力和灵活性。Intermine的设计目的是很容易地将其应用于生物学和生物体的其他领域。该项目的目的是将Intermine软件应用于上述五种MOD：小鼠、线虫、发芽酵母、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提供；所有MOD共同的标准界面；MOD之间更大的互操作性，以提供一套通用工具来比较和对比这组生物体内基因和蛋白质的性质，这是今天通常不具备的特征。该项目将在开发英国剑桥Intermine的团队和开发和维护五种MODS的团队之间进行合作，这些团队设在杰克逊实验室(MICE，MGI)、安大略省癌症研究所(线虫，WormBase)、斯坦福大学(YYEE，SGD)、威斯康星医学院(RAT，RGD)和俄勒冈大学(斑马鱼，ZFIN)。这项提议为每个站点提供一名工作人员，由此产生的团队将共同努力，将数据转移到将在每个国防部站点整合的Intermine数据库中，并向其中添加分析工具。以这种方式合作的一个好处是，一个地点的开发可以立即惠及其他地点。到项目结束时，MODS将能够为他们的研究社区提供更大的功能，更广泛的生物数据库社区将免费获得对支持Intermine软件的改进。拟议的项目在整合主要模式生物的实验结果方面是独一无二的。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是至关重要的。

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.