BioNLP Shared Task 2011

Overview

This page provides a brief summary of the BioNLP Shared Task 2011 and links to its resources. Please see also the BioNLP Shared Task 2011 home page.

The BioNLP Shared Task 2011 was collaboratively organized by many groups with an interest in biomedical domain information extraction. The GENIA Project coordinated the organization of the EPI and ID main tasks and the REL supporting task of the shared task, and the GE task annotations were based in part of the GENIA Event corpus annotations.

Corpus format

The various BioNLP Shared Task 2011 corpora are available in BioNLP Shared Task - flavored standoff format.

Documentation

For detailed documentation about the task, see the BioNLP Shared Task 2009 home page.

Publications

• Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan Nguyen, and Jun'ichi Tsujii. (2011). Overview of BioNLP Shared Task 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pages 1–6.

• Jin-Dong Kim, Yue Wang, Toshihisa Takagi, and Akinori Yonezawa. (2011). Overview of Genia Event Task in BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop, pages 7–15.

• Tomoko Ohta, Sampo Pyysalo, and Jun'ichi Tsujii. (2011). Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop, pages 16–25.

• Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun'ichi Tsujii, and Sophia Ananiadou. Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop, pages 26–35.

• Ngan Nguyen, Jin-Dong Kim, and Jun'ichi Tsujii. (2011). Overview of the Protein Coreference task in BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop, pages 74–82.

• Sampo Pyysalo, Tomoko Ohta, and Jun'ichi Tsujii. (2011). Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop, pages 83–88.

• Pontus Stenetorp, Goran Topić, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, and Jun'ichi Tsujii. (2011). BioNLP Shared Task 2011: Supporting Resources. Proceedings of BioNLP Shared Task 2011 Workshop, pages 112–120.

Download

• • The various shared task corpora are available from the BioNLP Shared Task 2011 download page.

  • A rich set of supporting analyses for the task generated by various tools are available from the BioNLP Shared Task 2011 supporting analyses download page.