  This paper describes an initial dataset and automatic natural language
processing (NLP) method for extracting concepts related to precision oncology
from biomedical research articles. We extract five concept types: Cancer,
Mutation, Population, Treatment, Outcome. A corpus of 250 biomedical abstracts
were annotated with these concepts following standard double-annotation
procedures. We then experiment with BERT-based models for concept extraction.
The best-performing model achieved a precision of 63.8%, a recall of 71.9%, and
an F1 of 67.1. Finally, we propose additional directions for research for
improving extraction performance and utilizing the NLP system in downstream
precision oncology applications.
