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Bioinformatics Advance Access originally published online on March 31, 2005
Bioinformatics 2005 21(11):2785-2786; doi:10.1093/bioinformatics/bti401
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

GandrKB—ontological microarray annotation and visualization

Daniel Schober 1,*, Ulf Leser 2, Martin Zenke 3 and Jens Reich 1

1Department for Bioinformatics, Max Delbrück Center for Molecular Medicine D-13122 Berlin Germany
2Institute for Computer Science, Humboldt-Universität D-10099 Berlin, Germany
3Institute for Biomedical Engineering-Cell Biology, Universitätsklinikum Aachen RWTH, 52057 Aachen, Germany

*To whom correspondence should be addressed.

Summary: The Gandr (gene annotation data representation) knowledgebase is an ontological framework for laboratory-specific gene annotation. Gandr uses Protégé 2000 for editing, querying and visualizing microarray data and annotations. Genes can be annotated with provided, newly created or imported ontological concepts. Annotated genes can inherit assigned concept properties and can be related to each other. The resulting knowledgebase can be visualized as interactive network of nodes and edges representing genes and their functional relationships. This allows for immediate and associative gene context exploration. Ontological query techniques allow for powerful data access.

Availability: GandrKB is platform independent and available free of charge either as web-application or as download from http://www.bioinf.mdc-berlin.de

Contact: schober{at}mdc-berlin.de

Supplementary information: http://www.bioinf.mdc-berlin.de/~schober/GandrIntro/


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