The mouse atlas database project

In the Edinburgh Mouse Atlas Project at the MRC Human Genetics Unit we have developed an on-line digital atlas describing how the mouse embryo develops from the single fertilized egg through to the fully developed embryo. The purpose is to support research into the mechanisms by which the genes control the development process and to provide a better understanding of congenital abnormalities and some cancers. The system provides a database that can be used by biomedical research to enable better use of data, more refined hypotheses and avoid repetition of lab experiments.||The emphasis for this project is the use of this resource for more extensive biomedical research on specific systems, in particular the development of the kidney and links to human development. In addition this cross-disciplinary programme involves novel work in image processing, databases and computing.

The Edinburgh Mouse Atlas Project (EMAP) has developed a digital space and time framework to support the study of the genetic control of embryo development. This framework is now the de facto standard for mouse embryo and forms the basis of a number of gene-expression databases including the Edinburgh Mouse Atlas Gene Expression (EMAGE) database in the MRC Human Genetics Unit. This is an active and rapidly growing database of in situ gene-expression patterns at all stages of development in the mouse and allows researchers to submit, query and analyse data from many sources. In the first instance it acts as an index for gene-expression data and includes original data that would otherwise not be accessible. This means that data can be more easily be located and shared which will reduce experimental repetition. This resource is now in place, freely accessible and in regular use for research and teaching.||The programme we propose extends the existing framework with special emphasis on using the resource for translational research and studies. In particular we have established a series of collaborations to study all aspects of uro-genital development and to link the mouse-atlas databases to human data. This will mean that the data generated throughout the world on mouse embryogenesis can be used to support studies of clinical importance. The uro-genital programme of research is part of two large funded projects to capture, analyse and provide a database of data relevant to a deep understanding of the development process and the cause of mutations and abnormalities. The interoperability with human is through studies of the normal development at The Centre For Life, Newcastle, and on abnormal development here in the Human Genetics Unit.||To support this research we are formalising and extending the existing framework to enable more sophisticated and complex query, interoperability and automated workflow. For this we are using the emerging semantic web and grid infrastructures to allow secure interoperability, data management and virtual organisations. In addition we undertake original research on the image processing and data mapping aspects of the problem.||Finally, with the new computational techniques we will extend the atlas framework to higher resolution in space and time with better understanding of biological space in the context of the database.