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@ehazlett
Created July 25, 2011 16:27
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Search PubMed with BioPython
#!/usr/bin/env python
# numpy and biopython are required -- pip install numpy biopython
from Bio import Entrez
from Bio import Medline
MAX_COUNT = 10
TERM = 'Tuberculosis'
print('Getting {0} publications containing {1}...'.format(MAX_COUNT, TERM))
Entrez.email = 'A.N.Other@example.com'
h = Entrez.esearch(db='pubmed', retmax=MAX_COUNT, term=TERM)
result = Entrez.read(h)
print('Total number of publications containing {0}: {1}'.format(TERM, result['Count']))
ids = result['IdList']
h = Entrez.efetch(db='pubmed', id=ids, rettype='medline', retmode='text')
records = Medline.parse(h)
authors = []
for record in records:
au = record.get('AU', '?')
for a in au:
if a not in authors:
authors.append(a)
authors.sort()
print('Authors: {0}'.format(', '.join(authors)))
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