sudo easy_install pip
pip3 install -r requirements.txt
python3 main.py
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Please hit 'select' file
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Please select a RPDR format or CSV format file to be searched by the program.
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Select the column names of patient id and report text for CSV format file
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Type in the label names and keywords/regex (separated by ',') and press the "Run Regex" button. If you only have one label, leave the Label_2, Label_3 unclick/blank
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To modify the highlighted text spans, please select the label radiobutton and select the note text, and then hit "Add" or "Delete"
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The program will then go through each note. Press "Save" or hit "Next" at the top of the screen
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Repeat this through each note until the end of the file
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You can also select an output CSV file to continue the annotation by pressing the "Load annotation" button
| patient id | report text | L1_spans | L1_text | L2_spans, if applicable | .... |
|---|---|---|---|---|---|
| 12345678 | sample text | 1,5|15,20|100,300 | cancer|CANCER|Carcinoma | 200,250 | .... |