Syntactic dependency based heuristics for biological event extraction

Authors:
Halil Kilicoglu;Sabine Bergler
Affiliations:
Concordia University, West Montréal, Canada;Concordia University, West Montréal, Canada
Venue:
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Year:
2009

Citing 14
Cited 16

Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
A shallow parser based on closed-class words to capture relations in biomedical text

Journal of Biomedical Informatics
Accurate unlexicalized parsing

ACL '03 Proceedings of the 41st Annual Meeting on Association for Computational Linguistics - Volume 1
Extracting human protein interactions from MEDLINE using a full-sentence parser

Bioinformatics
Coarse-to-fine n-best parsing and MaxEnt discriminative reranking

ACL '05 Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics
Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach

Artificial Intelligence in Medicine
RelEx---Relation extraction using dependency parse trees

Bioinformatics
Negation of protein–protein interactions

Bioinformatics
Integrating co-occurrence statistics with information extraction for robust retrieval of protein interactions from Medline

BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Postnominal prepositional phrase attachment in proteomics

BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
A graph kernel for protein-protein interaction extraction

BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Recognizing speculative language in biomedical research articles: a linguistically motivated perspective

BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Statistical anaphora resolution in biomedical texts

COLING '08 Proceedings of the 22nd International Conference on Computational Linguistics - Volume 1
Learning the scope of negation in biomedical texts

EMNLP '08 Proceedings of the Conference on Empirical Methods in Natural Language Processing

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
Two strong baselines for the BioNLP 2009 event extraction task

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
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
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
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 Genia event task in BioNLP Shared Task 2011

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
Learning local content shift detectors from document-level information

EMNLP '11 Proceedings of the Conference on Empirical Methods in Natural Language Processing
Modality and negation: An introduction to the special issue

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

Computational Linguistics
Enhancing search: events and their discourse context

CICLing'13 Proceedings of the 14th international conference on Computational Linguistics and Intelligent Text Processing - Volume 2

Quantified Score

Hi-index	0.00

Visualization

Abstract

We explore a rule-based methodology for the BioNLP'09 Shared Task on Event Extraction, using dependency parsing as the underlying principle for extracting and characterizing events. We approach the speculation and negation detection task with the same principle. Evaluation results demonstrate the utility of this syntax-based approach and point out some shortcomings that need to be addressed in future work.