Paper: PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations

ACL ID W12-2410
Title PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations
Venue Workshop on Biomedical Natural Language Processing
Session
Year 2012
Authors

Recent efforts in biomolecular event extrac- tion have mainly focused on core event types involving genes and proteins, such as gene expression, protein-protein interactions, and protein catabolism. The BioNLP?11 Shared Task extended the event extraction approach to sub-protein events and relations in the Epi- genetics and Post-translational Modifications (EPI) and Protein Relations (REL) tasks. In this study, we apply the Turku Event Ex- traction System, the best-performing system for these tasks, to all PubMed abstracts and all available PMC full-text articles, extract- ing 1.4M EPI events and 2.2M REL relations from 21M abstracts and 372K articles. We introduce several entity normalization algo- rithms for genes, proteins, protein complexes and protein components, aiming to uniquely ide...