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Releasing species in spaces: Waxholm Space and its connection to other model systems.

Fons Verbeek1*, Dome Potikanond1, Peng Yang1, A. Alia2, Herman Spaink3, Jyl Boline4 and Ilya Zavlavsky5
  • 1 Leiden University, Leiden Institute of Advanced Computer Science, Netherlands
  • 2 Leiden University, Leiden Institute of Chemistry, Netherlands
  • 3 Leiden University, Leiden Institute of Biology, Netherlands
  • 4 Informed Minds, Inc., United States
  • 5 San Diego Supercomputer Center, United States

The Waxholm is space specifically developed for interoperability in the rodent mouse brain (hawrylycz et al., 2009). Model systems are used in terms for their possibilities of high-throughput applications. In vertebrate research the zebrafish and medaka are good candidates in high-throughput analysis. This is extremely valuable in applications where one intends to screen large component libraries as zebrafish embryos (brittijn er al., 2009) can be obtained in large amounts and are easily processed. Interoperability amongst species is a long whished item developmental and related biology research (verbeek et al., 1999). The interpretation of the results is important in the field of zebrafish research, however, only if it can be related to higher vertebrates it will gain importance tremendously. In order to understand effects of compounds one needs a proper atlas in which data can be projected and effects on the phenotype can be understood. To relate effects to the higher vertebrates, so that ultimately a prediction to human can be made, the step from the zebrafish to the rodent need be made first. For the zebrafish a number of atlases (http://bio-imaging.liacs.nl/ZFAtlasServer/) and datasets are available. Defining interoperability between mouse and zebrafish is a challenging endeavor as it requires relating fish embryology with adult mouse; in the case of the high-throughput. Alternatively, a route via the adult zebrafish can be considered; here we have to use adult datasets in which the spatial resolution is much lower than the spatial resolution that can be accomplished in the embryo. Moreover, one has to consider the granularity of the annotations in datasets. Atlases are made to depict as much detail as possible, experimental data are not imaged with the highest possible resolution and compromise to resolution. All these effects have to be taken into account in finding a sensible interoperability between databases (belmamoune & verbeek, 2008). The INCF Digital Atlasing Program can contribute in accomplishing the interoperability in the Waxholm space by further extending services (zavlavsky, 2010). An effort has been made to extend these services. These services have been adapted and made congruent with services that are offered in Leiden. The attempt to map zebrafish data to mouse data via services stands as an interesting case study; it serves as a paradigm for future developments in interoperability of model systems. The INCF digital atlasing program is a community effort and requires input from the scientific community. A demonstration of early results will be given at the conference. Considerations on mapping of spatial data through ontological concepts are presented.

References

1. Hawrylycz M, et al. (2009) The INCF Digital Atlasing Program Report on Digital Atlasing Standards in the Rodent Brain. Nature Preceedings. Sebastiaan A. Brittijn, Suzanne J. Duivesteijn, Mounia Belmamoune, Laura F.M.Bertens, Wilbert Bitter, Joost D. de Bruijn, Danielle L. Champagne, Edwin Cuppen, Gert Flik, Christina M. Vandenbroucke-Grauls, Richard A.J. Janssen, Ilse M.L. de Jong, Edo Ronald de Kloet, Alexander Kros, Annemarie H. Meijer, Juriaan R. Metz, Astrid M. van der Sar, Marcel J.M. Schaaf, Stefan Schulte-Merker, Herman P. Spaink, Paul P. Tak, Fons J. Verbeek, Margriet J. Vervoordeldonk, Freek J. Vonk, Frans Witte,

2. Huipin Yuan and Michael K. Richardson (2009) Zebrafish development and regeneration: new tools for biomedical research. Int. J. Dev. Biol. (2009) 53: 835-850

3. Belmamoune M. and 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,

4. 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.

Conference: Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.

Presentation Type: Poster Presentation

Topic: Digital atlasing

Citation: Verbeek F, Potikanond D, Yang P, Alia A, Spaink H, Boline J and Zavlavsky I (2010). Releasing species in spaces: Waxholm Space and its connection to other model systems.. Front. Neurosci. Conference Abstract: Neuroinformatics 2010 . doi: 10.3389/conf.fnins.2010.13.00136

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Received: 18 Jun 2010; Published Online: 18 Jun 2010.

* Correspondence: Fons Verbeek, Leiden University, Leiden Institute of Advanced Computer Science, Leiden, Netherlands, fverbeek@liacs.nl