Developmental bioinformatics: linking genetic data to virtual embryos.
This paper discusses current efforts to produce databases of gene expression for the major model embryos used in developmental biology. The efforts to build these resources were motivated by the need for immediate internet access to all types of research data, and the production of these databases is 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 databases require the use of images to link molecular data with spatial information. In order to standardise database formats, digital atlases of some model systems are being produced that include integrated anatomical descriptions 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 images from serial sections. Next, we consider how to integrate textual and spatial descriptions of gene expression and the key tool needed to make this possible, i.e. anatomical nomenclature. A short review of internet resources on developmental biology is also given and future prospects for the development of these databases are discussed.
Verbeek
F J
FJ
Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Utrecht. verbeek@niob.knaw.nl
Lawson
K A
KA
Bard
J B
JB
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D015509:Developmental Biology / Q000379:methods*; D005314:Embryonic and Fetal Development / Q000235:genetics*; D015870:Gene Expression; D007091:Image Processing, Computer-Assisted; D020407:Internet; D008279:Magnetic Resonance Imaging; D018613:Microscopy, Confocal