A Phaeodactylum tricornutum literature database for interactive annotation of content

Phaeodactylum tricornutum is a widely used model organism for studying diatom biology. We created a P. tricornutum-specific literature database, or bibliome, that can be interactively annotated by users to improve the relevance and accuracy of search queries. A bibliome represents the current knowledge about a specific organism or biological process and is the foundation for genome-scale computation models. The bibliome of P. tricornutum was assembled from literature searches of ‘P. tricornutum’ (as topic) in two different existing databases, the Web of Knowledge and PubMed resulting in 2497 independent articles. We manually curated the bibliome for relevance to biochemical, physiological, and molecular biology studies. Literature that described the use of P. tricornutum as feed source and ecotoxicology studies were excluded from the bibliome. This process resulted in a final list of 1124 entries – 20% of which received additional classification in the form of notes or keywords. We present the bibliome in an HTML format that is easily searched and that can be customized according to the interests of individual researchers. This HTML tool can also easily be adapted for other algal species or specific research topics.