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

摘要

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 [3], a systematic nomenclature of the embryo anatomy, and defined 3D regions (domains) of the embryo. The reconstructions define a spatial framework for mapping data. Software has been developed to re-align serial sections and create a 3D voxel model of a mouse embryo which can be resectioned at any arbitrary 3D orientation and position so that experimental data can be mapped onto it [2]. The anatomical nomenclature is used as a controlled vocabulary for annotating and describing gene-expression patterns and is currently organised as a "part-of" hierarchy The notion of groups of anatomical terms is used to support alternative structuring of the hierarchy Anatomical domains are defined 3D regions and provide the mapping between the voxel model and the anatomical terms in the nomenclature.