Proceedings of the BioNLP Shared Task 2011 Workshop

The requirements of improved access to the massive amount of scientific literature in biomedical domain - through applications such as semantic search, assisted pathway annotation, and the automatic identification of specific biomolecular reactions for database curation support - place continuing demands on the development of methods and resources for advanced biomedical information extraction and text mining. The BioNLP Shared Task series seeks to advance this development through an increased focus on detailed structured representations of extracted information, novel corpus resources with fully text-bound annotation, and precise task definitions, support and evaluation. The BioNLP Shared Task 2011 is the second in the series, following up on the first event organized in 2009. Seeking to build on the success of the previous event, the task was organized as a collaboration between several groups in Asia, Europe and the US who defined in total eight specific tasks involving diverse challenges, including in addition to structured event extraction also relation extraction and supporting tasks such as coreference resolution. The main theme of the 2011 event was generalization, and the main tasks further broadened on the 2009 setup in three aspects: text types, subject domains, and novel event extraction targets. The task attracted broad interest from the community, and a total of 46 final submissions were received from 24 groups, maintaining the 2009 task participation numbers while nearly doubling its number of submissions. In addition to the continued interest from the biomedical text mining community, we were glad to welcome the participation of many new groups from academia and industry. The submissions demonstrated substantial progress at the established event extraction task and showed that event extraction methods generalize well, among other aspects, to full papers, new subject domains such as infectious diseases and bacterial interactions, and new sets of events such as protein post-translational modifications.