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BioPython ESearch XML File & Dates

Hi,

So I am attempting to do an esearch like the following in Biopython:

 handle = Entrez.esearch(
    db="pubmed",
    sort="relevance",
    term=disease,
    mindate=year,
    retmode="xml",
)
results = Entrez.read(handle) 
handle.close()

How would I go about returning this result as an xml file? Currently results = python dictionary of all the results but I would like to be able to output this as an xml file. So that I can use the file to plot a graph of some kind?

Also, I've put an min date to return the results of a specific year. I would like to know if it's possible to return results for a range of years?

search esearch
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written by chrisgbeldam • chrisgbeldam

1 answer

I did a quick scan of Bio.Entrez, and it doesn't seem to be equipped for writing eutils results as XML. I think it would be easier to build a eutils URL query and curl the results into a custom file.

As for the date, you can add it into your search term using ("<Start_date>"[PDAT] : "<end_date>"[PDAT])

Example: "Triple Negative Breast Cancer" AND ("2015/1/1"[PDAT] : "2016/1/1"[PDAT]) which becomes the URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="triple negative breast cancer" AND ("2015/1/1"[PDAT] : "2016/1/1"[PDAT])

Note: I cleaned up the URL so it would be easier to read, but I'm sure python can HTTP encode the readable URL (in this case by replacing (blank space) with %20 and " with %22

• 1 views • link
written by Ram Ram

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