Paper: From Pathways to Biomolecular Events: Opportunities and Challenges

ACL ID W11-0214
Title From Pathways to Biomolecular Events: Opportunities and Challenges
Venue Workshop on Biomedical Natural Language Processing
Session
Year 2011
Authors

The construction of pathways is a major fo- cus of present-day biology. Typical pathways involve large numbers of entities of various types whose associations are represented as reactions involving arbitrary numbers of reac- tants, 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 applica- ble for pathway annotation support. As a step toward realizing this possibility, we study the mapping from a formal pathway representa- tion to the event representation in order to identify remaining challenges in event extrac- tion for pathway annotation su...