Large-scale testing of bibliome informatics using Pfam protein families.

Abstract

Literature mining is expected to help not only with automatically sifting through huge biomedical literature and annotation databases, but also with linking bio-chemical entities to appropriate functional hypotheses. However, there has been very limited success in testing literature mining methods due to the lack of large, objectively validated test sets or "gold standards". To improve this situation we created a large-scale test of literature mining methods and resources. We report on a specific implementation of this test: how well can the Pfam protein family classification be replicated from independently mining different literature/annotation resources? We test and compare different keyt..