GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
Journal of Biomedical Informatics
Overview of BioNLP'09 shared task on event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Incorporating GENETAG-style annotation to GENIA corpus
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Distant supervision for relation extraction without labeled data
ACL '09 Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: Volume 2 - Volume 2
Bioinformatics
Bioinformatics
Complex event extraction at PubMed scale
Bioinformatics
Overview of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
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
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The construction of pathways is a major focus of present-day biology. Typical pathways involve large numbers of entities of various types whose associations are represented as reactions involving arbitrary numbers of reactants, outputs and modifiers. Until recently, few information extraction approaches were capable of resolving the level of detail in text required to support the annotation of such pathway representations. We argue that event representations of the type popularized by the BioNLP Shared Task are potentially applicable for pathway annotation support. As a step toward realizing this possibility, we study the mapping from a formal pathway representation to the event representation in order to identify remaining challenges in event extraction for pathway annotation support. Following initial analysis, we present a detailed study of protein association and dissociation reactions, proposing a new event class and representation for the latter and, as a step toward its automatic extraction, introduce a manually annotated resource incorporating the type among a total of nearly 1300 annotated event instances. As a further practical contribution, we introduce the first pathway-to-event conversion software for SBML/CellDesigner pathways and discuss the opportunities arising from the ability to convert the substantial existing pathway resources to events.