BioDEAL: Community generation of biological annotations

Abstract

Background. Publication databases in biomedicine (e.g., PubMed, MEDLINE) are growing rapidly in size every year, as are public databases of experimental biological data and annotations derived from the data. Publications often contain evidence that confirm or disprove annotations, such as putative protein functions, however, it is increasingly difficult for biologists to identify and process published evidence due to the volume of papers and the lack of a systematic approach to associate published evidence with experimental data and annotations. Natural Language Processing (NLP) tools can help address the growing divide by providing automatic high-throughput detection of simple terms in publication text. However, NLP tools are not mature enough to identify complex terms, relationships, or events. Results. In this paper we present and extend BioDEAL, a community evidence annotation system that introduces a feedback loop into the database-publication cycle to allow scientists to connect data-driven biological concepts to publications. Conclusion. BioDEAL may change the way biologists relate published evidence with experimental data. Instead of biologists or research groups searching and managing evidence independently, the community can collectively build and share this knowledge. © 2009 Breimyer et al; licensee BioMed Central Ltd.