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XenBase


NAR Molecular Biology Database Collection entry number 1151
Bowes, J.B.1, Snyder, K.A.1, Segerdell, E.2, Gibb, R.1, Jarabek, C.1, Noumen, E.1, Pollet, N.3, and Vize, P.D.1,2
1Department of Computer Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
2Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
3Laboratoire Developpement et Evolution, CNRS UMR 8080, Universite Paris-Sud, Orsay 91405, France

Database Description

Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. Data is collected from high-throughput screens, other databases, community submissions and scientific literature and integrated into a number of database modules covering subjects such as genes, gene expression, genomic analysis, literature and community. Searchable interfaces are provided for finding genes, publications, people, labs, organizations, Xenopus lines, and for browsing the X. tropicalis genome.

Recent Developments

Recent additions and improvements include a new gene expression section, literature and interactant tabs on gene pages, expansion of gene pages, identification of Xenopus gene mentions in literature, improved search and a stock center section.
The new gene expression section includes approximately 25,000 in situ gene expression images drawn from large scale screens, community submissions, and literature. We display over 1,000 gene expression images with captions from 7 different journals. Curators annotate images with stage and anatomy terms from the Xenopus Anatomy Ontology. This section also incorporates expression data from approximately 6 million ESTs. Users can currently access this data through the new expression tab on the gene page or through the expression search interface.
There is also now a literature tab linking to articles about the gene and an interactants tab showing potential gene interactants. A sophisticated link matching system has been added that identifies gene mentions (by symbol, name or synonym) in article titles, abstracts, or image captions. Gene mentions are hyper-linked from abstracts or captions in the literature section to their appropriate gene pages. These links from genes to literature underpin the literature and interactants tabs. Mentions of genes in image captions are also used to partially automate the annotation of those images.
An advanced gene search interface has been added. Auto-completion and suggestions have been implemented, and the option to search all Xenbase content for text has also been added. In conjunction with the European Xenopus Resource Centre (EXRC) we have added a stock center section. This lists data on frog lines that can be acquired from the EXRC.

Acknowledgements

This database is supported by NICHD R01 HD045776.
Developments in the Xenbase stock centre section are supported by the Wellcome Trust and BBSRC BB/F020627/1.

References

1. Bowes, J.B., Snyder, K.A., Segerdell, E., Gibb, R., Jarabek, C., Noumen, E., Pollet, N., and Vize, P.D. (2008) Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 36, D761-72. Segerdell, E., Bowes, J.B., Pollet, N., and Vize, P.D. (2008) An ontology for Xenopus anatomy and development. BMC Dev Biol. 8, 92


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