Add triples converter

my_experiments/ibd_literature/test.txt

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+Subject	Predicate	Object
+inflammatory bowel disease	pro-inflammatory	cytokine production
+ulcerative colitis	to	arachidonic acid metabolic process
+ulcerative colitis	relieving	inflammatory response
+ulcerative colitis	and	inflammatory response

output_parser_yaml.py

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+import yaml
+from yaml import CLoader as Loader
+from oaklib import get_adapter
+
+NULL_VALS = ['', 'Not mentioned', 'none mentioned', 'Not mentioned in the text', 
+             'Not mentioned in the provided text.', 'No exposures mentioned in the text.', 
+             'None', 'N/A', 'No exposures mentioned in the text.', 'None mentioned in the text', 
+             'Not mentioned in the text.', 'None relevant', 'None mentioned in the text.', 
+             'No gene to molecular activity relationships mentioned in the text.',
+             'No genes mentioned', 'No genes mentioned in the text.', 'NA', '-',
+             'None mentioned']
+output_file = "experiments/ibd_literature/output_2000_1122.yaml"
+
+def filter_dictionary(input_dict, filter_keys):
+    filtered_dict = {key: value for key, value in input_dict.items() if key in filter_keys}
+    return filtered_dict
+
+with open(output_file, 'r') as file:
+    filtered_data = []
+    for doc in yaml.safe_load_all(file):
+        try:
+            for dict in doc["extracted_object"]["disease_cellular_process_relationships"]:
+                filtered_data.append(filter_dictionary(dict, ["subject", "predicate", "object"]))
+        except:
+            continue
+
+for entry in filtered_data:
+    if (len(entry) == 3 and
+        entry["subject"] not in NULL_VALS and
+        entry["predicate"] not in NULL_VALS and
+        entry["object"] not in NULL_VALS):
+        if (entry["subject"].startswith("MONDO:") and
+            entry["object"].startswith("GO:")):
+            entry["subject"] = get_adapter("sqlite:obo:MONDO").label(entry["subject"])
+            # if entry["predicate"].startswith("RO:"):
+            #     entry["predicate"] = get_adapter("sqlite:obo:RO").label(entry["predicate"])
+            entry["object"] = get_adapter("sqlite:obo:GO").label(entry["object"])
+            if entry["predicate"].startswith("RO:"):
+                entry["predicate"] = get_adapter("sqlite:obo:RO").label(entry["predicate"])
+            print(entry)