Annotating Relations to Events in Bioscience Abstracts

Molecular events are central to molecular biology. An important type of event is the interaction between proteins. PML interacts with Tif1alpha (10610177)1 is a clause that denotes such an interaction. The written language of molecular biology contains discussions of such interactions, their precursers, their ramifications, evidence for them, etc. In the work reported on here, we focus on relations between such protein interactions and other elements. We annotated relations between such clauses and syntactic units either preceeding or following them. We focused on marking text coherency relations, using the inventory of coherency relations discussed in (Kehler, 2002). We discuss how such discourse-level information aids the automatic construction of molecular pathway representations, features of our data set, the discourse annotation exercise we performed, and ways of automating the extraction of such discourse-level information from bioscience literature. All examples in the paper are from abstracts available at the Nation Library of Medicine PubMed webpage (currently http://www.ncbi.nlm.nih.gov/PubMed/). The PubMed identifier is provided following each sentence and searching for this number as a key word will retrieve the corresponding abstract.