--- a
+++ b/utils/jsonl_to_csv.py
@@ -0,0 +1,90 @@
+import json
+import re
+
+def jsonl_to_csv(input_filepath, output_filepath, annotation_type, annotation_type_name):
+    with open(input_filepath, 'r', encoding='utf-8') as file:
+        jsonl_data = [json.loads(line) for line in file]
+
+    with open(output_filepath, 'w', encoding='utf-8') as file:
+        for entry in jsonl_data:
+            text = entry['text'].replace('\n', ' ').replace('\\r\\n', ' ').replace('\\n', ' ').replace('\\r', ' ')
+            entities = [e for e in entry['entities'] if e['label'] == annotation_type_name]
+            entities.sort(key=lambda e: e['start_offset']) #sort by start offset
+            
+            tokens = re.findall(r"\w+|\w+(?='s)|'s|['\".,!?;]", text, re.UNICODE) #split on spaces, keep punctuation
+            
+            current_pos = 0
+            entity_index = 0
+            tags = ''
+            for token in tokens:
+                start_offset = text.find(token, current_pos)
+                end_offset = start_offset + len(token)
+                current_pos = end_offset
+
+                tag = 'O'
+                if entity_index < len(entities):
+                    entity = entities[entity_index]
+                    if start_offset == entity['start_offset']:
+                        tag = 'B-' + annotation_type
+                    elif start_offset > entity['start_offset'] and end_offset <= entity['end_offset']:
+                        tag = 'I-' + annotation_type
+                    if end_offset == entity['end_offset'] and entity_index < len(entities) - 1:
+                        entity_index += 1
+
+                if tags == "":
+                    tags = f"{tags}{tag}"
+                else:
+                    tags = f"{tags} {tag}"
+
+            file.write(f"{text[:-1]}|{tags}\n")
+
+import argparse
+
+parser = argparse.ArgumentParser(
+        description='This script is used to convert JSONL data into CSV format.')
+
+parser.add_argument('-o', '--output', type=str, default="all.csv",
+                    help='Choose where to save the file after modifying.')
+parser.add_argument('-i', '--input', type=str, default="all.jsonl",
+                    help='Choose the file to modify.')
+parser.add_argument('-t', '--type', type=str, required=True,
+                    help='Specify the type of annotation to process. Type of annotation needs to be one of the following: Medical Condition, Symptom, Medication, Vital Statistic, Measurement Value, Negation Cue, Medical Procedure')
+
+args = parser.parse_args()
+
+if not args.output.endswith('.csv'):
+    raise ValueError('Output file needs to be defined as a CSV-file')
+
+if not args.input.endswith('.jsonl'):
+    raise ValueError('Input file needs to be defined as a JSONL-file')
+
+if args.type not in ['Medical Condition', 'Symptom', 'Medication', 'Vital Statistic', 'Measurement Value', 'Negation Cue', 'Medical Procedure']:
+    raise ValueError('Type of annotation needs to be one of the following: Medical Condition, Symptom, Medication, Vital Statistic, Measurement Value, Negation Cue, Medical Procedure')
+
+if args.type == 'Medical Condition':
+    annotation_type = 'MEDCOND'
+    annotation_type_name = 'Medical Condition'
+elif args.type == 'Symptom':
+    annotation_type = 'SYMPTOM'
+    annotation_type_name = 'Symptom'
+elif args.type == 'Medication':
+    annotation_type = 'MEDICATION'
+    annotation_type_name = 'Medication/Treatment'
+elif args.type == 'Vital Statistic':
+    annotation_type = 'VITALSTAT'
+    annotation_type_name = 'Vital Statistic'
+elif args.type == 'Measurement Value':
+    annotation_type = 'MEASVAL'
+    annotation_type_name = 'Measurement Value'
+elif args.type == 'Negation Cue':
+    annotation_type = 'NEGATION'
+    annotation_type_name = 'Negation Cue'
+elif args.type == 'Medical Procedure':
+    annotation_type = 'PROCEDURE'
+    annotation_type_name = 'Medical Procedure'
+else:    
+    raise ValueError('Type of annotation needs to be one of the following: Medical Condition, Symptom, Medication, Vital Statistic, Measurement Value, Negation Cue, Medical Procedure')
+
+jsonl_to_csv(args.input, args.output, annotation_type, annotation_type_name)
+
+print(f"Conversion of {args.input} to {args.output} for type \"{annotation_type_name}\" completed.")