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Abstract
Xenbase (www.xenbase.org) is the model organism database for Xenopus tropicalis and Xenopus laevis, two frog species used as model systems for developmental and cell biology. Xenbase curation processes centre on associating papers with genes and extracting gene expression patterns. Papers from PubMed with the keyword 'Xenopus' are imported into Xenbase and split into two curation tracks. In the first track, papers are automatically associated with genes and anatomy terms, images and captions are semi-automatically imported and gene expression patterns found in those images are manually annotated using controlled vocabularies. In the second track, full text of the same papers are downloaded and indexed by a number of controlled vocabularies and made available to users via the Textpresso search engine and text mining tool.
Figure 1. The Xenbase literature curation process splits into two streams. The first stream consists of a series of manual and automated steps that are used to annotate gene expression patterns in papers. The second stream describes the automated processes of capturing, transforming, inputting, and indexing papers into the Textpresso search engine.
Figure 2. The Xenbase image curation interface consists of two panels. The left panel shows the image, caption and a tables of existing annotations made to that image. The right side of the panel contains a form used for editing existing or new annotations. It starts with a series of fields to specify species, gene name, clone names or accessions. Next the curator can specify a range of development stages when a particular expression pattern occurs. Finally, anatomy terms describing where expression occurs can be chosen from checkbox lists of commonly uses anatomy terms or a suggestion box. Anatomy terms are restricted to those that exist during the stage range previously entered by the curator. Finally, there is a section for updating the curation status of the item and entering curation notes.
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