Bioinformatics beyond sequence: mapping gene function in the embryo

The concept of a bioinformatic framework is exemplified by sequence databases. DNA sequences provide a one-dimensional framework to which additional information concerning structure and function can be added. Additional frameworks are being developed, such as controlled vocabularies and ontologies, so that information about gene expression and function can be indexed and compared between experiments and between organisms. Frameworks are being developed at many levels of biological organization, such as gene sequence, protein structure, metabolic pathway and organism. Organism-level frameworks are essential for comparison of gene expression and function in development. Such frameworks can be textual or can be digital spatio-temporal models of development. One such framework is being constructed by the Edinburgh Mouse Atlas Project (EMAP). Additional frameworks are being developed in other model systems, such as zebrafish. EMAP at present provides a reference framework to identify and name parts of the embryo, and a framework to which gene expression data can be mapped. This allows comparisons to be made between gene expression patterns. Future goals of this work will be to map other types of data, such as phenotypic data on mouse mutants, and to integrate data with similar frameworks in other model systems.