Paper: Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature

ACL ID W14-3402
Title Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature
Venue Proceedings of the BioNLP Shared Task 2013 Workshop
Session
Year 2014
Authors

In this paper, we present a system for recognizing temporal expressions related to cell cycle phase (CCP) concepts in biomedical literature. We identified 11 classes of cell cycle related temporal ex- pressions, for which we made extensions to TIMEX3, arranging them in an on- tology derived from the Gene Ontology. We annotated 310 abstracts from PubMed. Annotation guidelines were developed, consistent with existing time-related anno- tation guidelines for TimeML. Two anno- tators participated in the annotation. We achieved an inter-annotator agreement of 0.79 for an exact span match and 0.82 for relaxed constraints. Our approach is a hybrid of machine learning to recognize temporal expressions and a rule-based ap- proach to map them to the ontology. We trained a named entity recognizer usi...