Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Extracting regulatory gene expression networks from PubMed
ACL '04 Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics
RelEx---Relation extraction using dependency parse trees
Bioinformatics
Extracting relation information from text documents by exploring various types of knowledge
Information Processing and Management: an International Journal
Kernel approaches for genic interaction extraction
Bioinformatics
High-performance gene name normalization with GeNo
Bioinformatics
A graph kernel for protein-protein interaction extraction
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Learning relations from biomedical corpora using dependency trees
KDECB'06 Proceedings of the 1st international conference on Knowledge discovery and emergent complexity in bioinformatics
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
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
Towards semantic annotation supported by dependency linguistics and ILP
ISWC'10 Proceedings of the 9th international semantic web conference on The semantic web - Volume Part II
BioNLP '11 Proceedings of BioNLP 2011 Workshop
Towards exhaustive protein modification event extraction
BioNLP '11 Proceedings of BioNLP 2011 Workshop
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
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
A pattern approach for biomedical event annotation
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
Generalizing biomedical event extraction
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
A framework for biological event extraction from text
Proceedings of the 2nd International Conference on Web Intelligence, Mining and Semantics
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We describe the approach to event extraction which the JulieLab Team from FSU Jena (Germany) pursued to solve Task 1 in the "BioNLP'09 Shared Task on Event Extraction". We incorporate manually curated dictionaries and machine learning methodologies to sort out associated event triggers and arguments on trimmed dependency graph structures. Trimming combines pruning irrelevant lexical material from a dependency graph and decorating particularly relevant lexical material from that graph with more abstract conceptual class information. Given that methodological framework, the JulieLab Team scored on 2nd rank among 24 competing teams, with 45.8% precision, 47.5% recall and 46.7% F1-score on all 3,182 events.