Developmental bioinformatics: linking genetic data to virtual embryos

Citation
Fj. Verbeek et al., Developmental bioinformatics: linking genetic data to virtual embryos, INT J DEV B, 43(7), 1999, pp. 761-771
Citations number
48
Categorie Soggetti
Cell & Developmental Biology
Journal title
INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY
ISSN journal
02146282 → ACNP
Volume
43
Issue
7
Year of publication
1999
Pages
761 - 771
Database
ISI
SICI code
0214-6282(1999)43:7<761:DBLGDT>2.0.ZU;2-6
Abstract
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.