Agreement rate data set for GENETEX manuscript

Objectives: Clinico-Genomic Data (CGD) acquired through routine
clinical practice has the potential to improve our understanding of
clinical oncology. However, these data often reside in heterogeneous and
semi-structured data, resulting in prolonged time-to-analyses. Materials
and Methods: We created GENETEX: an R package and Shiny
application for text mining genomic reports from EHR and direct import
into REDCap®. Results: GENETEX facilitates the abstraction of CGD
from EHR and streamlines capture of structured data into REDCap®. Its
functions include natural language processing of key genomic information,
transformation of semi-structured data into structured data and
importation into REDCap. When evaluated with manual abstraction, GENETEX
had >99% agreement and captured CGD in approximately one-fifth the
time. Conclusions: GENETEX is freely available under the
Massachusetts Institute of Technology license and can be obtained from
GitHub. GENETEX is executed in R and deployed as a Shiny application for
non-R users. It produces high-fidelity abstraction of CGD in a fraction of
the time.