Extending InterMine to yeast rat and zebrafish model organism databases

University Of Cambridge, Cambridge

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Abstract

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.