The Xenbase literature curation process

The Xenbase literature curation process by Jeff B. Bowes, Kevin A. Snyder, Christina James-Zorn, Virgilio G. Ponferrada, Chris J. Jarabek, Kevin A. Burns, Bishnu Bhattacharyya, Aaron M. Zorn and Peter D. Vize.


Xenbase ( 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.

Which curation workflow will work best for your topic map activities will depend upon a number of factors.

What would you adopt, adapt or alter from the curation workflow in this article?

How would you evaluate the effectiveness of any of your changes?

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