def pm2bib(pm): author = "; ".join(pm['AU']) year = pm['DP'][0:4] bib = """@article{PMID:%s, author = {%s}, title = {%s}, journal = {%s}, year = {%s}, volume = {%s}, number = {%s}, pages = {%s}, } """ % (pm['PMID'],author,pm['TI'],pm['TA'],year,pm['VI'],pm.get('IP',""),pm['PG']) return bib if __name__ == "__main__": from Bio import Entrez, Medline Entrez.email = "xxx@gmail.com" record = Entrez.read(Entrez.esearch(db="pubmed",term="biopython")) idlist = record["IdList"] records = Medline.parse(Entrez.efetch(db="pubmed",id=idlist,rettype="medline",retmode="text")) for record in records: print pm2bib(record)
Thursday, April 15, 2010
Make bib file from Pubmed-ID
Today, I wrote a code of making bib-file from pubmed in Python. HML.
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