Semantic querying over the biomedical literature has gained popularity, where a semantic representation of biomedical documents is required. Previous BioNLP Shared Tasks exercised semantic event extraction with a small number of pre-defined event concepts. The GRO task of the BioNLP’13-ST imposes the challenge of dealing with over 100 GRO concepts. Its annotated corpus consists of 300 MEDLINE abstracts, and an analysis of interannotator agreement on the annotations by two experts shows Kappa values between 43% and 56%. The results from the only participant are promising with F-scores 22% (events) and 63% (relations), and also lead us to open issues such as the need to consider the ontology structure.
['Jung-jae Kim', 'Xu Han', 'Vivian Lee', 'Dietrich Rebholz-Schuhmann']
GRO Task: Populating the Gene Regulation Ontology with events and relations