To obtain a comprehensive understanding of embryonic development, we need to characterize the anatomical, physiological, developmental, and molecular genetic properties of a wide range of different types of cells and test hypotheses that relate these properties functionally: How do genes regulate the specific properties of cells? For example, in the case of neurons, what determines the shape of a neuron and how does shape affect function? Do specific genes regulate where the first neuronal axons grow? Presently there is no straight forward method for obtaining all the data relevant to answering these questions.
Information about these diverse properties of embryos is being obtained from a variety of organisms. However, systematic organization of this information into databases and methods for rapid and easy access to such databases are still lacking; this hampers relating one property to another. Moreover, this is a world-wide problem [Fox94]: to integrate information from diverse labs in a timely fashion and to make it easily accessible to everyone in a meaningful manner that will truly promote scientific discovery. Such databases have been established for the gene sequence data generated by molecular biologists, but none adequately integrate the image data types required to characterize the morphology, antigenicity, and gene expression patterns of developing embryos. Progress will be greatly promoted by solutions to this problem.
Numbers of images available within the next year:Table 1. Estimates of disk space for zebrafish data within the next year. Total may double within 2-3 years. *Number of mutant alleles estimated at 350 from Eugene, 740 from Boston, 1450 from Tübingen. Storage of images estimated for 1300x1300 32-bit resolution, compressed with JPEG "good" compression level.Developmental whole-mounts 40 images 8 Mb staging atlas: sections (10 µm) 400 images 80 Mb
Anatomical atlas 50 sagital, 50 horizontal (10µm sections): 50 transverse 150 images 30 Mb
Adult brain atlas: 25 µm 3 views 600 images 120 Mb
Morphology of identified neurons: 45 types x 10 views 450 images 90 Mb
Mutant (genetic loci) 500 loci x 40 views 20000 images 4000 Mb anatomy atlases: (whole-mounts + sections)
Gene expression 150 genes x 40 views 6000 images 1200 Mb pattern atlases: (whole-mounts + sections)Numbers of text files:
Publications: 3120; over 100 in the past year 280 Mb Genes: 150 80 Mb Mapped markers: 560; 3600 anticipated within 2 years 100 Mb People: 709 presently 30 Mb Mutant alleles: 282; >2,000* expected by next year 25 Mb
The zebrafish is a vertebrate in which embryonic development can be studied with very high precision; yet there is still a complete lack of a comprehensive database for zebrafish. Although zebrafish use in genetic research is relatively new, the number of labs and the amount of data generated by these labs are increasing at a phenomenal rate; the information already far exceeds the ability of individual scientists to track and organize it (Table 1). Moreover, the absence of a consensus for representing different types of data is leading to inconsistencies in the way that data is stored by different labs. An organized and concerted effort is desperately needed to establish a database for the zebrafish community.
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