apibioinformaticsbiopythonpubmed

How to get the latest papers from pubmed

This is a bit of a specific question, but somebody must have done this before. I would like to get the latest papers from pubmed. Not papers about a certain subjects, but all of them. I thought to query depending on modification date (mdat). I use biopython.py and my code looks like this

handle = Entrez.egquery(mindate='2015/01/10',maxdate='2017/02/19',datetype='mdat')
results = Entrez.read(handle)
for row in results["eGQueryResult"]:
        if row["DbName"]=="nuccore":
            print(row["Count"])

However, this results in zero papers. If I add term='cancer' I get heaps of papers. So the query seems to need the term keyword... but I want all papers, not papers on a certain subjects. Any ideas how to do this? thanks carl

Solution

  • term is a required parameter, so you can't omit it in your call to Entrez.egquery.

    If you need all the papers within a specified timeframe, you will probably need a local copy of MEDLINE and PubMed Central:

    For MEDLINE, this involves getting a license. For PubMed Central, you can download the Open Access subset without a license by ftp.