Nucleic Acids Research, 2010, Vol. 38, Database issue D609 Figure 2. Modal dialog of gene expression information. When a thumbprint image is selected by the user, a modal dialog box is launched illustrating an enlarged view and additional data. To enhance usability, users can select XAO search terms by clicking checkboxes of commonly searched terms or by using a suggestion box that allows users to search for tissues by their XAO term or common synonyms. A suggestion box lists possible match terms as the user types. When the user selects an anatomy term, it appears in a list to the right of the search box. Users can drill-down to more speciﬁc terms by clicking the plus sign to the left of a tissue and examine parts of the tissue. In this manner, the user can ﬁnd speciﬁc search terms without strong knowledge of the anatomy ontology. After executing the search, the user is presented with a list of expression pattern results organized by the gene (or clone, if unmapped). The results include which stages and XAO terms were matched for each gene or clone. Searching for a particular tissue will return items annotated to parts of that tissue. For example, a search for pronephric kidney will also return results annotated to the glomerulus. From the initial search results, the user can drill-down to experiments matching their search criteria and then detailed information on each experiment. Xenbase gene expression evidence is drawn from expressed sequence tags (ESTs), in situ hybridization and immunohistochemistry assays. For EST evidence, genes are aligned to ESTs from particular tissues at speciﬁc development stages. Gene expression images come from three sources: literature, large scale screens and community submissions. Images extracted from papers with the per- mission of publishers are manually curated and associated with genes, tissues and development stages based on infor- mation in the image caption and article content. For older literature that we have scraped images from, we have performed an automated ﬁrst pass of curation. Using the link-matching system, we identify gene names and synonyms in the captions. If a single gene is mentioned in the caption we also search for the use of XAO tissue terms or their synonyms. We then infer that the single gene mentioned must be expressed in all of the identiﬁed tissues. Development stage descriptions vary too much to extract them using automated means. Therefore, stages for these expression patterns are set to ‘unspeciﬁed’. While imperfect, this process allows initial associations between uncurated literature gene expression images and genes (and possibly XAO tissues). These liter- ature images will be manually curated as time permits. The largest block of expression images come from two large in situ screens AxelDB (6) and XDB3 (Naoto Ueno, NIBB, Okazaki, Japan), consisting of 2600 and 18 600 images, respectively. The Axeldb images are annotated by the development stage and often contain tissue anno- tation. The XDB3 images were only annotated with