[Published October 1998 in Bioinformatics 14(9) Pages 807-814. Full text available in PDF format]

Zomit: biological data visualization and browsing

Stuart Pook1,2, Guy Vaysseix1,3 and Emmanuel Barillot1,3

1 GIS Infobiogen, 7 rue Guy Môquet - BP 8, 94801 Villejuif cedex, France, 2 École Nationale Supérieure des Télécommunications, Département Informatique et Réseaux, 46 rue Barrault, 75013 Paris, France and 3 Généthon, 1 bis rue de l'Internationale, 91000 Évry, France

Received on April 16, 1998; revised on July 7, 1998; accepted on July 9, 1998

Abstract

Motivation: The problems caused by the difficulty in visualizing and browsing biological databases have become crucial. Scientists can no longer interact directly with the huge amount of available data. However, future breakthroughs in biology depend on this interaction. We propose a new metaphor for biological data visualization and browsing that allows navigation in very large databases in an intuitive way. The concepts underlying our approach are based on navigation and visualization with zooming, semantic zooming and portals; and on data transformation via magic lenses. We think that these new visualization and navigation techniques should be applied globally to a federation of biological databases.

Results: We have implemented a generic tool, called Zomit, that provides an application programming interface for developing servers for such navigation and visualization, and a generic architecture-independent client (JavaTM applet) that queries such servers. As an illustration of the capabilities of our approach, we have developed ZoomMap, a prototype browser for the HuGeMap human genome map database.

Availability: Zomit and ZoomMap are available at the URL http://www.infobiogen.fr/services/zomit.

Contact: stuart@infobiogen.fr

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