BioNLP Shared Task 2009

Overview

This page provides a brief summary of the BioNLP Shared Task 2009 and links to its resources. Please see also the BioNLP Shared Task 2009 home page.

The BioNLP Shared Task 2009 was organized by GENIA Project and its corpora were curated based on the annotations of the publicly available GENIA Event corpus and an unreleased (blind) section of the GENIA Event corpus annotations, used for evaluation.

Corpus format

The corpus is 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, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun'ichi Tsujii. (2009). Overview of BioNLP'09 Shared Task on Event Extraction. Proceedings of the Workshop on BioNLP: Shared Task, pages 1–9.

• Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun'ichi Tsujii. (2011). Extracting Bio-Molecular Events From Literature -- The BioNLP'09 Shared Task. Computational Intelligence, Volume 27, Number 4, 2011, pages 513 -- 540.

Download

• • Sample Data: bionlp09_shared_task_sample_data_rev3.tar.gz

    • Contains a small sample of shared task data.

  • Training Data: bionlp09_shared_task_training_data_rev2.tar.gz

    • The primary training data of the shared task.

  • Development Data: bionlp09_shared_task_development_data_rev1.tar.gz

    • Data for testing in system development; includes gold standard annotation.

  • Test Data: bionlp09_shared_task_test_data_without_gold_annotation.tar.gz

    • Test data without gold standard annotation. To evaluate on this data, use the online evaluation service.

  • Evaluation Tools: bionlp09_shared_task_evaluation_tools_v1.tar.gz

    • Tools for offline evaluation against gold standard annotation.

  • Annotation subset generator: generate-task-specific-a2-file_pl

    • Script for generating a subset of annotations relevant to a subtask.

  • Standoff format checker: standoff-check_pl

    • Script for format checking for the a2 files.

  • Annotation viewer: eventview_pl

    • Simple text-based event annotation viewer.