---
title: "Overview of BioNLP Shared Task 2011 — Kim 2011"
description: "BioNLP-ST 2011 was the second round of a community challenge on fine-grained biomedical… 34 references, cited by 66 papers here."
authors: ["Jin-Dong Kim", "Sampo Pyysalo", "Tomoko Ohta", "Robert Bossy", "Ngan Nguyen", "Jun'ichi Tsujii"]
year: 2011
venue: "Proceedings of BioNLP Shared Task 2011 Workshop"
source: "https://aclanthology.org/W11-1801/"
licence: "CC BY-NC-SA 3.0 (ACL Anthology, before 2016)"
licence_url: "https://creativecommons.org/licenses/by-nc-sa/3.0/"
summary_licence: "Elamur Cosmic License"
canonical: "https://research.elamur.ai/free/en/papers/kim-2011-overview-bionlp-shared-task-2011/"
---
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# Overview of BioNLP Shared Task 2011

**Authors:** [Jin-Dong Kim](https://md.research.elamur.ai/free/en/authors/jin-dong-kim/), [Sampo Pyysalo](https://md.research.elamur.ai/free/en/authors/sampo-pyysalo/), [Tomoko Ohta](https://md.research.elamur.ai/free/en/authors/tomoko-ohta/), [Robert Bossy](https://md.research.elamur.ai/free/en/authors/robert-bossy/), [Ngan Nguyen](https://md.research.elamur.ai/free/en/authors/ngan-nguyen/) and [Jun'ichi Tsujii](https://md.research.elamur.ai/free/en/authors/jun-ichi-tsujii/) · **Year:** 2011 · **Venue:** [Proceedings of BioNLP Shared Task 2011 Workshop](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/) ([BioNLP Shared Task Workshop 2011](https://md.research.elamur.ai/free/en/venues/bionlp-workshop-and-shared-task/2011/)) · **Publisher:** [Association for Computational Linguistics](https://md.research.elamur.ai/free/en/publishers/association-for-computational-linguistics/) · **Licence:** [CC BY-NC-SA 3.0 (ACL Anthology, before 2016)](https://creativecommons.org/licenses/by-nc-sa/3.0/)

**Links:** [Publisher's page](https://aclanthology.org/W11-1801/) · [PDF](https://aclanthology.org/W11-1801.pdf) · [OpenAlex](https://openalex.org/W76749362)

**Citations:** 223 citations (OpenAlex, 2026-10-14) · [66](https://md.research.elamur.ai/free/en/papers/kim-2011-overview-bionlp-shared-task-2011/cited-by/) in our library, of the 141,840 papers whose bibliographies we read

## Summary
BioNLP-ST 2011 was the second round of a community challenge on fine-grained biomedical information extraction, especially event extraction. The 2009 edition relied only on the Genia corpus, which covers one narrow subdomain and comes from one group. This edition was run jointly by several groups to test whether extraction methods generalize in three directions: text type, event type, and subject domain. It offered five main tasks: GE, EPI, ID, and the bacteria track tasks BB and BI. It also offered three supporting tasks meant to help with them: CO (protein coreference), REL (entity relations) and REN (gene renaming). Over about six months, 24 teams sent 46 final submissions. On the repeated GE abstract task, systems cut errors by more than 10% compared with 2009. Performance on full papers and new domains fell only slightly. BI beat the earlier LLL result by about 20 F-score points. One goal failed: no team used supporting-task outputs in its main-task systems.

## Key points
- Text types widened from abstracts to full papers (GE, ID) and web pages (BB). The number of targeted event/relation types was GE 9, EPI 15, ID 10, BB 2 and BI 10.
- EPI added 14 event types (protein/DNA modifications and their reversals) and two new argument roles, Sidechain and Contextgene. ID added four entity types, including CHEMICAL and ORGANISM, plus a category for high-level biological processes.
- The best GE abstract F-score rose to 57.46, from 51.95 in 2009. Full papers reached 53.14, and three teams beat the strongest earlier result (Miwa et al., 2010b).
- Per the results table, other best F-scores were roughly IDf 55.59, EPIf 53.33, BB 45, BI 77, CO 34.05, REL 57.70 and REN 87.00.
- UTurku was the only team to enter all eight tasks. Seventeen of the 24 teams entered just one task.

## Interesting ideas
- **Keep a frozen benchmark next to new data.** GE reused the exact 2009 task definition and abstract set while adding a full-paper set. This lets one task measure both year-over-year progress and transfer to a new text type, which is useful for any recurring benchmark, such as a Ukrainian NLP evaluation.
- **Use subtask views to isolate difficulty.** Comparing the same event type across tasks (GE vs EPI PHOSPHORYLATION) shows whether a domain shift itself hurts results. Splitting tasks into core and full versions separates trigger and core-argument extraction from extra-argument extraction.
- **Choose supporting tasks from error analysis.** CO was created because the 2009 analysis showed coreference was blocking event extraction. Building auxiliary tasks around measured failure points is a principled way to design a challenge.
- **Stage the schedule.** Supporting tasks ran and finished first so their outputs could feed the main tasks. The paper reports this produced no actual uptake and suggests the long, complex setup overloaded teams. The lesson is that organizers should keep the burden low if they want participants to combine resources.
- **Provide gold entities to narrow the focus.** Giving gold named-entity annotation lets participants concentrate on relation and event extraction. BB, which required teams to recognize entities themselves, scored lower, which shows the cost of removing that help.

*Our summary of the paper, in our own words — not its text. The work belongs to its authors; read it at the links above.*

## Institutions

- [Microsoft Research Asia](https://md.research.elamur.ai/free/en/companies/microsoft-research-asia/) — Company, Beijing, China · 54 works · 59,921 citations
- [The University of Tokyo](https://md.research.elamur.ai/free/en/universities/the-university-of-tokyo/) — University, Tokyo, Japan · 45 works · 8,692 citations

Also on the byline: [Database Center for Life Science](https://ror.org/018q2r417).

📚 Shelves (4): [🧬 Biochemistry, Genetics and Molecular Biology](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/) · 116 works · [🧬 Molecular Biology](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/molecular-biology/) · 114 works · [🎯 Decision Sciences](https://md.research.elamur.ai/free/en/shelves/decision-sciences/) · 85 works · [🎯 Information Systems and Management](https://md.research.elamur.ai/free/en/shelves/decision-sciences/information-systems-and-management/) · 18 works

## Cite

Cite as: 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.

The paper itself, not this page. BibTeX from the library's record of the work.

```bibtex
@inproceedings{kim2011overview,
  title = {{Overview of BioNLP Shared Task 2011}},
  author = {Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan Nguyen and Jun'ichi Tsujii},
  booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop},
  year = {2011},
  url = {https://aclanthology.org/W11-1801/}
}
```

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## References

34 references, 2 of them with a card of ours. ↗ leads to the work, «find» searches for one we have no id for yet.

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2. Sophia Ananiadou, Dan Sullivan, William Black, Gina-Anne Levow, Joseph J. Gillespie, Chunhong Mao, Sampo Pyysalo, BalaKrishna Kolluru, Junichi Tsujii, and Bruno Sobral. 2011. Named entity recognition for bacterial type IV secretion systems. PLoS ONE, 6(3):e14780. [find](https://scholar.google.com/scholar?q=Sophia+Ananiadou%2C+Dan+Sullivan%2C+William+Black%2C+Gina%2DAnne+Levow%2C+Joseph+J%2E+Gillespie%2C+Chunhong+Mao%2C+Sampo+Pyysalo%2C+BalaKrishna+Kolluru%2C+Junichi+Tsujii%2C+and+Bruno+Sobral%2E+2011%2E+Named+entity+recognition+)
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*Updated 24 October 2026*