Published online 1 November 2009 Nucleic Acids Research, 2010, Vol. 38, Database issue D607–D612 doi:10.1093/nar/gkp953 Xenbase: gene expression and improved integration Jeff B. Bowes1,*, Kevin A. Snyder1, Erik Segerdell1, Chris J. Jarabek 1 , Kenan Azam1, Aaron M. Zorn2 and Peter D. Vize1 1Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada and 2Division of Developmental Biology Cincinnati Children’s Research Foundation and University of Cincinnati Department of Pediatrics, College of Medicine. Cincinnati, OH 45229, USA Received September 16, 2009; Accepted October 12, 2009 ABSTRACT Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community infor- mation for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog pages. New content has been added including a section on gene expression patterns that incorporates image data from the lit- erature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expres- sion search interface. The gene catalog has grown to contain over 15 000 genes. Collaboration with the European Xenopus Research Center (EXRC) has resulted in a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and the clearing- house for Xenopus gene nomenclature. The African frogs Xenopus laevis and X. (Silurana) tropicalis serve as a powerful and widely used model system for exploring gene function in vertebrate develop- ment. Both species have unique experimental advantages and combining data from the two synergistically enhances their usefulness. Many of the genes and fundamental mechanism governing early embryonic development were ﬁrst discovered in the Xenopus system. Xenopus females generate thousands of embryos in response to a simple hormone injection and the large robust embryos are simple to microinject with mRNA or anti-sense reagents. As the embryos develop a full set of diﬀerentiated organs within days of fertilization, very rapid high-throughput screens of gene function can be performed. Xenbase (www.xenbase.org) is a free, publicly accessible resource, for Xenopus data, amalgamating data from both of these Xenopus species and linking to both Xenopus and other model organism resources. Xenbase also manages the Xenopus Anatomical Ontology (XAO) (1) and acts as a clearinghouse for Xenopus gene names. Additionally, Xenbase maintains the biological data for the European Xenopus Resource Centre (EXRC). Xenbase has been growing. Since our last report in 2008 (2), the count of genomic features in Xenbase has grown from 486 000 records to 4 750 000, including ESTs, cDNA clones, mRNA, Ensembl (3) gene models and alignment matches. 26 000 images have been added and Xenopus publications have increased from 35 000 to 38 000. The initial release of Xenbase included a gene catalog, the GBrowse genome browser (4), a literature compen- dium, a community directory, a blast search and extensive links to orthologous species gene records at NCBI and other model organism databases. Since then, eﬀorts have focused on integration of the literature and the gene catalog, incorporating gene expression data, expanding the gene catalog, adding support for the EXRC and making numerous improvements to search and usability. LITERATURE, LINK MATCHING AND INTERACTANTS The literature section is now much more strongly leveraged in Xenbase. As a result of the development of a link-matching system, it has been possible to integrate the literature section with the gene catalog and mine it for potential interactants. Finally, through agreements with publishers, the literature section has become a key part of Xenbase’s gene expression coverage by incorporating published images that illustrate gene expression patterns. With 38 000 articles in Pubmed mentioning Xenopus, complete manual curation was impossible. A link- matching system was developed that searches for the presence of gene symbols, synonyms and names in the *To whom correspondence should be addressed. Tel: +1 403 220-2824; Fax: +1 403 284-4707; Email: bowes@ucalgary.ca The Author(s) 2009. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.