Discovering protein similarity using natural language processing.

Extracting protein interaction relationships from textual repositories, such as MEDLINE, may prove useful in generating novel biological hypotheses. Using abstracts relevant to two known functionally related proteins, we modified an existing natural language processing tool to extract protein interaction terms. We were able to obtain functional information about two proteins, Amyloid Precursor Protein and Prion Protein, that have been implicated in the etiology of Alzheimer's Disease and Creutzfeldt-Jakob Disease, respectively.