This paper discusses current efforts to produce databases of gene expressio
n for the major model embryos used in developmental biology. The efforts to
build these resources were motivated by the need for immediate internet ac
cess to all types of research data, and the production of these databases i
s a major and new challenge for bioinformatics. Thus far bioinformatics has
mainly been concerned with textually oriented resources and data, much of
it concerned with gene and protein sequences. Because the genetic basis of
developmental biology is integrated with developmental anatomy, these datab
ases require the use of images to link molecular data with spatial informat
ion. In order to standardise database formats, digital atlases of some mode
l systems are being produced that include integrated anatomical description
s and these are being linked to appropriate genetic data. Integrating such
image-based, searchable data into databases makes new demands on the field
of bioinformatics and we consider here the imaging modalities that are used
to obtain information and we discuss in particular the production of 3D im
ages from serial sections. Next, we consider how to integrate textual and s
patial descriptions of gene expression and the key tool needed to make this
possible, i.e. anatomical nomenclature. A short review of internet resourc
es on developmental biology is also given and future prospects for the deve
lopment of these databases are discussed.