Searching PubMed with Python

[Update 30Nov09] The Bio.EUtils module has been replaced by Bio.Entrez. This means that the following code and links will no longer work. However, see the comments at the end of the email where readers have posted updated code.

Given a DOI or PMID, how can you find metadata for a publication using Python? The EUtils module of BioPython, by Andrew Dalke, is your friend.

For a DOI, you need to do a search:

from Bio import EUtils
from Bio.EUtils import DBIdsClient

doi = "10.1016/j.jmb.2007.02.065"

client = DBIdsClient.DBIdsClient()
result = client.search(doi + "[aid]", retmax = 1)
summary = result[0].summary()

For a PMID, there's a more direct method:

from Bio import EUtils
from Bio.EUtils import DBIdsClient

PMID = "17238260"
result = DBIdsClient.from_dbids(EUtils.DBIds("pubmed", PMID))
summary = result[0].summary()

So, what can you do with the summary? Something like the following maybe:

>>> data = summary.dataitems
>>> print data.keys()
['DOI', 'Title', 'Source', 'Volume', ...., ]
>>>  print "%s. %s %s %s, %s, %s." % (
...  ", ".join(data['AuthorList'].allvalues()),
...  data['Title'], data['Source'], data['PubDate'].year,
...  data['Volume'], data['Pages'])
...
O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. Using
reaction mechanism to measure enzyme similarity. J Mol Biol
2007, 368, 1484-99.

For more info:

• PubMed search terms
• Bio.EUtils
• Andrew's introduction to (an earlier version of) Bio.EUtils