Added code to scrape records from PubMed

pubmed/pubmed_scrape.py

@@ -0,0 +1,96 @@
+from Bio import Entrez
+
+def fetch_pubmed_records(email, search_term, max_records=100):
+    """
+    Fetch PubMed records matching the search term.
+
+    Parameters:
+        email (str): Email address for NCBI.
+        search_term (str): The term to search for in PubMed.
+        max_records (int): Maximum number of records to fetch.
+
+    Returns:
+        list: List of PubMed IDs (PMIDs).
+    """
+    Entrez.email = email
+    handle = Entrez.esearch(db="pubmed", term=search_term, retmax=max_records)
+    record = Entrez.read(handle)
+    handle.close()
+    id_list = record["IdList"]
+    return id_list
+
+def fetch_pubmed_details(id_list):
+    """
+    Fetch detailed information for a list of PubMed IDs.
+
+    Parameters:
+        id_list (list): List of PubMed IDs.
+
+    Returns:
+        dict: Parsed XML data with detailed information for each PubMed ID.
+    """
+    ids = ",".join(id_list)
+    handle = Entrez.efetch(db="pubmed", id=ids, rettype="xml", retmode="xml")
+    data = Entrez.read(handle)  # Read the data using Entrez.read
+    handle.close()
+    return data
+
+def extract_pubmed_info(records):
+    """
+    Extract required information from PubMed records.
+
+    Parameters:
+        records (dict): Parsed XML data from PubMed.
+
+    Returns:
+        list: List of dictionaries with extracted information.
+    """
+    extracted_data = []
+    for record in records['PubmedArticle']:
+        medline_citation = record.get('MedlineCitation', {})
+        article = medline_citation.get('Article', {})
+        journal = article.get('Journal', {})
+        journal_issue = journal.get('JournalIssue', {})
+        pub_date = journal_issue.get('PubDate', {})
+
+        # Extract article information
+        article_info = {
+            "Title": article.get("ArticleTitle", ""),
+            "Abstract": ' '.join(article.get("Abstract", {}).get("AbstractText", [])),
+            "PublicationDate": pub_date.get("Year", ""),
+            "Authors": [f"{author.get('LastName', '')} {author.get('ForeName', '')}" for author in article.get("AuthorList", [])],
+            "Journal": journal.get("Title", ""),
+            "PMID": medline_citation.get("PMID", ""),
+        }
+        extracted_data.append(article_info)
+    return extracted_data
+
+def main():
+    """
+    Main function to fetch, parse, and print PubMed data.
+    """
+    email = "[email protected]"  # Replace with your email
+    search_term = "COVID-19"  # Replace with your search term
+    max_records = 100  # Adjust the number of records to fetch
+
+    print("Fetching PubMed records...")
+    id_list = fetch_pubmed_records(email, search_term, max_records)
+
+    print(f"Found {len(id_list)} records. Fetching details...")
+    records = fetch_pubmed_details(id_list)
+
+    print("Extracting information from records...")
+    extracted_data = extract_pubmed_info(records)
+
+    # Print or save the extracted data
+    for data in extracted_data:
+        print(f"PMID: {data['PMID']}")
+        print(f"Title: {data['Title']}")
+        print(f"Abstract: {data['Abstract']}")
+        print(f"Publication Date: {data['PublicationDate']}")
+        print(f"Authors: {', '.join(data['Authors'])}")
+        print(f"Journal: {data['Journal']}")
+        print("\n")
+
+if __name__ == "__main__":
+    main()