The Edinburgh mouse atlas and gene-expression database: a spatio-temporal database for biological research

The Edinburgh Mouse Atlas Project (EMAP) has developed a digital atlas of mouse development which provides a bioinformatics framework to spatially reference biological data. The EMAP core database contains 3D grey-level reconstructions of the mouse embryo at various stages of development, a systematic nomenclature of the embryo anatomy, and defined 3D regions (domains) of the embryo. The reconstructions define a spatial framework for mapping data. Data front an in-situ gene-expression database is spatially mapped onto the atlas allowing the users to query gene-expression patterns using the 3D embryo model as a reference. The mouse atlas and gene-expression databases are publicly accessible through a set of Web-based tools. The system consists of a set of tools and databases, some of which reside locally on the Mouse Atlas hosts, others are remote. The middleware layer is primarily CORBA-based, but also makes use of Java servlets. Data are primarily stored in an object-oriented database system (ObjectStore). As a public bioinformatics resource, the Mouse Atlas system must be easily accessible to researchers all over the world, hence interoperability is a key issue. The Mouse Atlas is an on-going research and development project at the Medical Research Council, Human Genetics Unit, in Edinburgh. Access to its databases and further information is available through its Web site.