Shallow semantic parsing of randomized controlled trial reports.

In this work, we are measuring the performance of Propbank-based Machine Learning (ML) for automatically annotating abstracts of Randomized Controlled Trials (CTRs) with semantically meaningful tags. Propbank is a resource of annotated sentences from the Wall Street Journal (WSJ) corpus, and we were interested in assessing performance issues when porting this resource to the medical domain. We compare intra-domain (WSJ/WSJ) with cross-domain (WSJ/medical abstract) performance. Although the intra-domain performance is superior, we found a reasonable cross-domain performance.

Towards semantic role labeling & IE in the medical literature.

INTRODUCTION: In this work, we introduce the concept of semantic role labeling to the medical domain. We report first results of porting and adapting an existing resource, Propbank, to the medical field. Propbank is an adjunct to Penn Treebank that provides semantic annotation of predicates and the roles played by their arguments. The main aim of this work is the applicability of the Propbank frame files to predicates typically encountered in the medical literature. METHODS: We analyzed a target corpus of 610,100 abstracts, which was selected by searching for publication type "case reports". From this target corpus, we randomly selected 10,000 sample abstracts to estimate the predicate distribution, and matched the predicates from this sample to the predicates in Propbank. RESULTS: Of the 1998 unique verbs in our sample, 76% were represented in Propbank. This included the 40 most frequent verbs, which represented 49% of all predicate instances in our sample and which matched the Propbank usage in a study of representative sentences. We propose extensions to Propbank that handle medical predicates, which are not adequately covered by Propbank. CONCLUSION: We believe that semantic role labeling using Propbank is a valid approach to capture predicate relations in the medical literature.

Incorporation of clinical practice guidelines for glaucoma into an ophthalmology electronic medical record.

Clinical practice guidelines represent the best current thinking on the management of acute and chronic medical conditions. Unfortunately, the implementation of such guidelines in clinical practice has been difficult and problematic. Electronic medical records represent an opportunity to implement guidelines. We have designed a system for incorporating guidelines for the management of glaucoma into an ophthalmology EMR.