Integrated Annotation For Biomedical Information Extraction

We describe an approach to two areas of biomedical information extraction, drug development and cancer genomics. We have developed a framework which includes corpus annotation integrated at multiple levels: a Treebank containing syntactic structure, a Propbank containing predicate-argument structure, and annotation of entities and relations among the entities. Crucial to this approach is the proper characterization of entities as relation components, which allows the integration of the entity annotation with the syntactic structure while retaining the capacity to annotate and extract more complex events. We are training statistical taggers using this annotation for such extraction as well as using them for improving the annotation process.