Create pubmed.py

pubmed.py

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+# libraries
+from datasets import load_dataset
+import os
+import json 
+
+# load all of pubmed -- note that this dataset is 360GB+, so I'm loading this in "streaming mode" -- https://huggingface.co/docs/datasets/stream
+# https://huggingface.co/datasets/pubmed
+full_pubmed = load_dataset('/home/sagemaker-user/pubmed_dataset_src/', streaming=True)
+
+# make directory if it doesn't exist
+if not os.path.isdir('pubmed_portions'):
+    os.mkdir('pubmed_portions')
+
+# download pubmed in portions
+portion_size = 1000 # 1 mil entries per portion
+pubmed_portion = []
+counter = 0
+
+# note that I'm only taking the pmid, year, abstract text, abstract title, and authors. There is some more information that you can see by either visiting (https://huggingface.co/datasets/pubmed) or printing one of the entries in the dataset
+for idx, entry in enumerate(full_pubmed['train']): 
+    try:
+        # print(entry)
+        pmid = entry['MedlineCitation']['PMID']
+        year = entry['MedlineCitation']['DateCompleted']['Year']
+        abstract_text = entry['MedlineCitation']['Article']['Abstract']['AbstractText']
+        abstract_title = entry['MedlineCitation']['Article']['ArticleTitle']
+        abstract_authors_list = entry['MedlineCitation']['Article']['AuthorList']['Author']['LastName']
+
+        if len(abstract_text) > 20 and len(abstract_title) > 5 and len(abstract_authors_list) > 0: # check that the abstract text, title, or authors are not empty
+            pubmed_portion.append({'pmid':pmid, 'year':year, 'abstract_text':abstract_text, 'abstract_title':abstract_title, 'abstract_authors_list':abstract_authors_list})
+
+        if idx % 10000 == 0:
+            print('idx', idx)
+
+        if idx % portion_size == 0 and len(pubmed_portion)>0:
+            # save the pubmed portion
+            with open(f'pubmed_portions/pubmed_portion_{counter}.json', 'w') as fp:
+                json.dump(pubmed_portion, fp)        
+            # reset the list
+            pubmed_portion = []
+            counter += 1
+    except: # any issue with the article
+        pass