Xenbase: expansion and updates of the Xenopus model organism database

Abstract

Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus and Xenopus data to workers using other model organisms. As an amphibian Xenopus serves as a useful evolutionary bridge between invertebrates and more complex vertebrates such as birds and mammals. Xenbase content is collated from a variety of external sources using automated and semi-automated pipelines then processed via a combination of automated and manual annotation. A link-matching system allows for the wide variety of synonyms used to describe biological data on unique features, such as a gene or an anatomical entity, to be used by the database in an equivalent manner. Recent updates to the database include the Xenopus laevis genome, a new Xenopus tropicalis genome build, epigenomic data, collections of RNA and protein sequences associated with genes, more powerful gene expression searches, a community and curated wiki, an extensive set of manually annotated gene expression patterns and a new database module that contains data on over 700 antibodies that are useful for exploring Xenopus cell and developmental biology.

Figure 1.

The Xenbase gene expression annotation interface. An image, or panel of images is loaded. After selecting the species and developmental stage, common anatomical terms appropriate for this stage range are loaded. If a term needed, in this example, otic placode, does not appear, the curator types the term in the ‘anatomy Item(s)’ text field. Once three letters have been typed AJAX generates a list of suggestions that the curator then selects from and the ID appended to the image. Often element names corresponding to adult structures are used by authors, for example kidney, rather than the stage appropriate name for the item at the time it is shown, which in an early embryo may be ‘pronephric mesenchyme' as in this example. The system enforces correct stage appropriate term usage.

Figure 2.

Manual annotation data are displayed along with literature figures and legends. For each image curated from the literature the legend along wit Xenbase annotations are displayed. Often these are quite different due to the use of legacy gene names in the literature or non-standard anatomical terminology. In this example the ‘t' gene is called ‘xbra' in the legend. No detailed anatomical data are present in the figure legend, but have been added by curators and can now be found using the various query systems in the Gene Expression Search toolset.