Nick Burton

EMAGE: Electronic Mouse Atlas of Gene Expression

The EMAGE (Electronic Mouse Atlas of Gene Expression) database (http://www.emouseatlas.org/emage) allows users to perform on-line queries of mouse developmental gene expression. EMAGE data are represented spatially using a framework of 3D mouse embryo models, thus allowing uniquely spatial queries to be carried out alongside more traditional text-based queries. This spatial representation of the data also allows a comparison of spatial similarity between the expression patterns. The data are mapped to the models by a team of curators using bespoke mapping software, and the associated meta-data are curated for accuracy and completeness. The data contained in EMAGE are gathered from three main sources: from the published literature, through large-scale screens and collaborations, and via direct submissions from researchers. There are a variety of ways to query the EMAGE database via the on-line search interfaces, as well as via direct computational script-based queries. EMAGE is a free, on-line, community resource funded by the Medical Research Council, UK.

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.

Developing the eHistology Atlas.

The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook ‘The Atlas of Mouse Development’ by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php

3D mouse embryo model: EMA38, Stage TS16, Age E10.0 (est)

The eMouseAtlas team have generated a series of 3D images to capture mouse embryo development and to use as a spatial framework for gene-expression and other spatially organised data. The resource is published and available on the Web at http://www.emouseatlas.org/emap/ema/.

3D mouse embryo model: EMA80, Stage TS23, Age E15.0 (est)

The eMouseAtlas team have generated a series of 3D images to capture mouse embryo development and to use as a spatial framework for gene-expression and other spatially organised data. The resource is published and available on the Web at http://www.emouseatlas.org/emap/ema/.