The Ontology of developmental anatomy of zebrafish

Following the production of a 3D digital atlas of zebrafish development a controlled vocabulary for the zebrafish developmental anatomy was compiled. This controlled vocabulary is entended with relations by which it turned into a genuine ontology. Several tools have ben developed to view the content of the ontology.

Database of zebrafish developmental anatomy ontology
[Zebrafish Anatomy Database]

A database of the zebrafish ontology was designed to be able to manage patterns of gene expression. The database was originally designed as an Informix Dynamic Server database. As of the beginning of 2009 it was transferred to a mySQL database. The application will start in a new window and the interface should be self-explanotory. For any problems with the Java-applet first check the java=console in your browser.

Application to browse anatomical terms including pictures
[AnatomyBrowsing JavaScript Demo]

Restricted set is used in this javascript demonstration program.
The application will start in a new window.

Application to browse ontology (java 2)
[AnatomyBrowsing Java Demo]

Restricted set is used in this java demonstration program.
The application will start in a new window.


Verbeek, F.J., den Broeder,M.J., Boon, P.J., Buitendijk, B., van Raaij, E.J., Doerry, E., Zivkovic, D. (2000) A Standard 3D digital Atlas of Zebrafish Embryonic Development for Projection of Experimental Data. Proceedings SPIE 3964, Internet Imaging I, 242-252.

Verbeek, F.J., Lawson, K.A., and Bard, J.B.L. (1999). Developmental BioInformatics: linking genetic data to virtual embryos. Int.J.Dev.Biol. 43, 761-771.

Bei, Y., Dmitrieva, J., Belmamoune, M., Verbeek, F.J. (2007)
Ontology Driven Image Search Engine.
Proc. SPIE Vol. 6506, MultiMedia Content Access: Algorithms & Systems (Eds Hanjalic, A., Schettini, R., Sebe, N.), 65060G-1,65060G-10

Belmamoune M. and Fons J. Verbeek, F.J. (2008)
Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database.
Journal of Integrative BioInformatics, 5(2):92, 2008

Belmamoune, M. (2009)
Spatio-Temporal Framwork for Inegrative Analysis of Zebrafish developmental Studies.
PhD Thesis, Leiden University. ISBN 978-90-9024866

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