Extracting molecular binding relationships from biomedical text

Abstract

ARBITER is a Prolog program that extracts assertions about macromolecular binding relationships from biomedical text. We describe the domain knowledge and the underspecified linguistic analyses that support the identification of these predications. After discussing a formal evaluation of ARBITER, we report on its application to 491, 000 MEDLINE® abstracts, during which almost 25, 000 binding relationships suitable for entry into a database of macromolecular function were extracted.