--- a
+++ b/collated_tasks/tasks/get_abbreviations.py
@@ -0,0 +1,40 @@
+import argparse
+import spacy
+from scispacy.abbreviation import AbbreviationDetector
+from utils.get_text_from_csv import get_df, get_notes_single_row_id
+
+def get_abbreviations(model, text):
+    print(f"Identifying abbrevations using {model}")
+    partial_input = '\n'.join(text.split('\n')[:10])
+    print(f"Input text (truncated): {partial_input}\n...")
+    nlp = spacy.load(model)
+    # add the abbreviation pipe to spacy pipeline
+    nlp.add_pipe("abbreviation_detector")
+    doc = nlp(text)
+    return doc._.abbreviations
+
+if __name__ == "__main__":
+    # parse command line arguments
+    parser = argparse.ArgumentParser(description='Identify abbreviations in MIMIC EVENTNOTES')
+    parser.add_argument('--mimic_dir', default='../../tutorials/data/mimic_data/', type=str, help='directory to mimic data')
+    parser.add_argument('--model', default='en_core_sci_sm', type=str, help='model for spacy')
+    parser.add_argument('--row_id', default=178, type=int,  help='row id of text to be processed')
+    parser.add_argument('--output_file', default='./output_abbreviations.txt', type=str, help='output to save identified abbreviations')
+
+    args = parser.parse_args()
+    mimic_dir = args.mimic_dir
+    model = args.model
+    row_id = args.row_id
+    output_file = args.output_file
+    print(f"Data file: {mimic_dir}NOTEEVENTS.csv")
+
+    df = get_df(mimic_dir + 'NOTEEVENTS.csv')
+    text = get_notes_single_row_id(df, row_id)
+    abbreviations  = get_abbreviations(model, text)
+
+    with open(output_file, 'w') as f:
+        f.write("Abbreviation" + "\t\t" + "Definition\n")
+        for abrv in abbreviations:
+            #f.write(f"{abrv} \t ({abrv.start}, {abrv.end}) {abrv._.long_form}")
+            f.write(f"{abrv}\t\t{abrv._.long_form}\n")
+    print(f"Abbreviations written to {args.output_file}")