CODEWITHSUNDEEP
pythonpython-3.xbiopython
megadyptes
megadyptes

Reputation: 101

BioPython Pubmed Eutils url?

I'm trying to run some queries against Pubmed's Eutils service. If I run them on the website I get a certain number of records returned, in this case 13126 (link to pubmed).

A while ago I bodged together a python script to build a query to do much the same thing, and the resultant url returns the same number of hits (link to Eutils result).

Of course, not having any formal programming background, it was all a bit cludgy, so I'm trying to do the same thing using Biopython. I think the following code should do the same thing, but it returns a greater number of hits, 23303.

from Bio import Entrez
Entrez.email = "[email protected]"
handle = Entrez.esearch(db="pubmed", term="stem+cell[All Fields]",datetype="pdat", mindate="2012", maxdate="2012")
record = Entrez.read(handle)
print(record["Count"])

I'm fairly sure it's just down to some subtlety in how the url is being generated, but I can't work out how to see what url is being generated by Biopython. Can anyone give me some pointers?

Thanks!

EDIT:

It's something to do with how the url is being generated, as I can get back the original number of hits by modifying the code to include double quotes around the search term, thus:

handle = Entrez.esearch(db='pubmed', term='"stem+cell"[ALL]', datetype='pdat', mindate='2012', maxdate='2012')

I'm still interested in knowing what url is being generated by Biopython as it'll help me work out how i have to structure the search term for when i want to do more complicated searches.

Upvotes: 3

Views: 1037

Answers (2)

Peter Cock
Peter Cock

Reputation: 1614

You've solved this already (Entrez likes explicit double quoting round combined search terms), but currently the URL generated is not exposed via the API. The simplest trick would be to edit the Bio/Entrez/__init__.py file to add a print statement inside the _open function.

Update: Recent versions of Biopython now save the URL as an attribute of the returned handle, i.e. in this example try doing print(handle.url)

Upvotes: 1

buhtz
buhtz

Reputation: 12152

handle = Entrez.esearch(db="pubmed", term="stem+cell[All Fields]",datetype="pdat", mindate="2012", maxdate="2012")
print(handle.url)

Upvotes: 1

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