This tool overlays concepts / tokens extracted by UCSF CTAKES client with an original text.
To generate a visualization, run:
python ctakesvis.py [-html] [plain text: path/to/note.txt] [ctakes extract: path/to/note_combined_output.json]
python ctakesvis.py [plain text note] [directory of ctakes extract]
--recursive flag to make sure the tabulator javascript package is downloaded
git clone --recursive https://github.com/BCHSI/ctakesvis
cd ctakesvis
pip install -U .
the tool will output an Index page, which can come with summaries (e.g. counts of concepts per domain) if respective parameters are included
./ctakesvis.py samples/ samples-extracts/samples -a count -b domain -f cui
# -a : aggregate using count function
# -b : by column 'domain'
# -f : aggregate field 'cui' (any field works in this example for 'count' function)