Overview of BioNLP'09 shared task on event extraction

Authors:
Jin-Dong Kim;Tomoko Ohta;Sampo Pyysalo;Yoshinobu Kano;Jun'ichi Tsujii
Affiliations:
University of Tokyo, Tokyo, Japan;University of Tokyo, Tokyo, Japan;University of Tokyo, Tokyo, Japan;University of Tokyo, Tokyo, Japan;University of Tokyo, Tokyo, Japan and University of Manchester, Manchester, UK
Venue:
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Year:
2009

Citing 8
Cited 92

Intricacies of Collins' Parsing Model

Computational Linguistics
Coarse-to-fine n-best parsing and MaxEnt discriminative reranking

ACL '05 Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics
Self-training for biomedical parsing

HLT-Short '08 Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics on Human Language Technologies: Short Papers
Introduction to the bio-entity recognition task at JNLPBA

JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Static relations: a piece in the biomedical information extraction puzzle

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Incorporating GENETAG-style annotation to GENIA corpus

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
U-Compare

Bioinformatics
Porting a lexicalized-grammar parser to the biomedical domain

Journal of Biomedical Informatics

Extracting complex biological events with rich graph-based feature sets

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
A Markov logic approach to bio-molecular event extraction

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
High-precision biological event extraction with a concept recognizer

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Extraction of biomedical events using case-based reasoning

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Molecular event extraction from link grammar parse trees

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
A multi-phase approach to biomedical event extraction

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Supervised classification for extracting biomedical events

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Biomedical event detection using rules, conditional random fields and parse tree distances

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Analyzing text in search of bio-molecular events: a high-precision machine learning framework

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Exploring ways beyond the simple supervised learning approach for biological event extraction

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Static relations: a piece in the biomedical information extraction puzzle

BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Syntactic Parsing for Bio-molecular Event Detection from Scientific Literature

EPIA '09 Proceedings of the 14th Portuguese Conference on Artificial Intelligence: Progress in Artificial Intelligence
Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
OntoGene in BioCreative II.5

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Joint inference for knowledge extraction from biomedical literature

HLT '10 Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics
Using SVMs with the command relation features to identify negated events in biomedical literature

NeSp-NLP '10 Proceedings of the Workshop on Negation and Speculation in Natural Language Processing
SemEval-2010 task 8: Multi-way classification of semantic relations between pairs of nominals

SemEval '10 Proceedings of the 5th International Workshop on Semantic Evaluation
Linking SweFN++ with medical resources, towards a MedFrameNet for Swedish

Louhi '10 Proceedings of the NAACL HLT 2010 Second Louhi Workshop on Text and Data Mining of Health Documents
Two strong baselines for the BioNLP 2009 event extraction task

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Event extraction for post-translational modifications

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Scaling up biomedical event extraction to the entire PubMed

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
A comparative study of syntactic parsers for event extraction

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Arguments of nominals in semantic interpretation of biomedical text

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
An exploration of mining gene expression mentions and their anatomical locations from biomedical text

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Automatic construction and multi-level visualization of semantic trajectories

Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems
Towards event extraction from full texts on infectious diseases

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Integration of static relations to enhance event extraction from text

BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
The CoNLL-2010 shared task: learning to detect hedges and their scope in natural language text

CoNLL '10: Shared Task Proceedings of the Fourteenth Conference on Computational Natural Language Learning --- Shared Task
Detecting speculative language using syntactic dependencies and logistic regression

CoNLL '10: Shared Task Proceedings of the Fourteenth Conference on Computational Natural Language Learning --- Shared Task
A high-precision approach to detecting hedges and their scopes

CoNLL '10: Shared Task Proceedings of the Fourteenth Conference on Computational Natural Language Learning --- Shared Task
HedgeHunter: a system for hedge detection and uncertainty classification

CoNLL '10: Shared Task Proceedings of the Fourteenth Conference on Computational Natural Language Learning --- Shared Task
A simple ensemble method for hedge identification

CoNLL '10: Shared Task Proceedings of the Fourteenth Conference on Computational Natural Language Learning --- Shared Task
Evaluating the impact of alternative dependency graph encodings on solving event extraction tasks

EMNLP '10 Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing
Word sense disambiguation for event trigger word detection

DTMBIO '10 Proceedings of the ACM fourth international workshop on Data and text mining in biomedical informatics
Evaluating dependency representation for event extraction

COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Syntactic scope resolution in uncertainty analysis

COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Natural language query processing for life science knowledge

AMT'10 Proceedings of the 6th international conference on Active media technology
Visualization and language processing for supporting analysis across the biomedical literature

KES'10 Proceedings of the 14th international conference on Knowledge-based and intelligent information and engineering systems: Part IV
Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction

Journal of Biomedical Informatics
U-compare: A modular NLP workflow construction and evaluation system

IBM Journal of Research and Development
Event extraction as dependency parsing

HLT '11 Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies - Volume 1
Semantic parsing for biomedical event extraction

IWCS '11 Proceedings of the Ninth International Conference on Computational Semantics
EVEX: a pubmed-scale resource for homology-based generalization of text mining predictions

BioNLP '11 Proceedings of BioNLP 2011 Workshop
Fast and simple semantic class assignment for biomedical text

BioNLP '11 Proceedings of BioNLP 2011 Workshop
From pathways to biomolecular events: opportunities and challenges

BioNLP '11 Proceedings of BioNLP 2011 Workshop
Towards exhaustive protein modification event extraction

BioNLP '11 Proceedings of BioNLP 2011 Workshop
SimSem: fast approximate string matching in relation to semantic category disambiguation

BioNLP '11 Proceedings of BioNLP 2011 Workshop
Search-based structured prediction applied to biomedical event extraction

CoNLL '11 Proceedings of the Fifteenth Conference on Computational Natural Language Learning
Customizing an information extraction system to a new domain

RELMS '11 Proceedings of the ACL 2011 Workshop on Relational Models of Semantics
Biomedical events extraction using the hidden vector state model

Artificial Intelligence in Medicine
A parser-based approach to detecting modification of biomedical events

Proceedings of the ACM fifth international workshop on Data and text mining in biomedical informatics
Overview of BioNLP Shared Task 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of Genia event task in BioNLP Shared Task 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of the epigenetics and post-translational modifications (EPI) task of BioNLP Shared Task 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of the infectious diseases (ID) task of BioNLP Shared Task 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Biomedical event extraction from abstracts and full papers using search-based structured prediction

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Model combination for event extraction in BioNLP 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
BioNLP Shared Task 2011: bacteria gene interactions and renaming

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of the protein coreference task in BioNLP Shared Task 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of the entity relations (REL) supporting task of BioNLP Shared Task 2011

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
BioNLP Shared Task 2011: supporting resources

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Complex biological event extraction from full text using signatures of linguistic and semantic features

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Using Kybots for extracting events in biomedical texts

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Extracting biological events from text using simple syntactic patterns

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
From graphs to events: a subgraph matching approach for information extraction from biomedical text

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Adapting a general semantic interpretation approach to biological event extraction

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Generalizing biomedical event extraction

BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Stanford's multi-pass sieve coreference resolution system at the CoNLL-2011 shared task

CONLL Shared Task '11 Proceedings of the Fifteenth Conference on Computational Natural Language Learning: Shared Task
Fast and robust joint models for biomedical event extraction

EMNLP '11 Proceedings of the Conference on Empirical Methods in Natural Language Processing
Learning local content shift detectors from document-level information

EMNLP '11 Proceedings of the Conference on Empirical Methods in Natural Language Processing
Supervised machine learning approach for bio-molecular event extraction

SEMCCO'11 Proceedings of the Second international conference on Swarm, Evolutionary, and Memetic Computing - Volume Part II
A framework for biological event extraction from text

Proceedings of the 2nd International Conference on Web Intelligence, Mining and Semantics
Using an ensemble system to improve concept extraction from clinical records

Journal of Biomedical Informatics
Modality and negation: An introduction to the special issue

Computational Linguistics
Are you sure that this happened? assessing the factuality degree of events in text

Computational Linguistics
Did it happen? the pragmatic complexity of veridicality assessment

Computational Linguistics
Cross-genre and cross-domain detection of semantic uncertainty

Computational Linguistics
Kernel-Based logical and relational learning with klog for hedge cue detection

ILP'11 Proceedings of the 21st international conference on Inductive Logic Programming
Relation mining experiments in the pharmacogenomics domain

Journal of Biomedical Informatics
Hybrid pattern matching for complex ontology term recognition

Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Domain adaptation of a dependency parser with a class-class selectional preference model

ACL '12 Proceedings of ACL 2012 Student Research Workshop
A comparison of Chinese parsers for stanford dependencies

ACL '12 Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics: Short Papers - Volume 2
Event linking: grounding event reference in a news archive

ACL '12 Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics: Short Papers - Volume 2
PubMed-scale event extraction for post-translational modifications, epigenetics and protein structural relations

BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
Bridging the gap between scope-based and event-based negation/speculation annotations: a bridge not too far

ExProM '12 Proceedings of the Workshop on Extra-Propositional Aspects of Meaning in Computational Linguistics
Design and implementation of GXP make - A workflow system based on make

Future Generation Computer Systems
Automatic Identification and Classification of Noun Argument Structures in Biomedical Literature

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
ReliAble dependency arc recognition

Expert Systems with Applications: An International Journal
Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts

Journal of Biomedical Informatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

The paper presents the design and implementation of the BioNLP'09 Shared Task, and reports the final results with analysis. The shared task consists of three sub-tasks, each of which addresses bio-molecular event extraction at a different level of specificity. The data was developed based on the GENIA event corpus. The shared task was run over 12 weeks, drawing initial interest from 42 teams. Of these teams, 24 submitted final results. The evaluation results are encouraging, indicating that state-of-the-art performance is approaching a practically applicable level and revealing some remaining challenges.