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The code for the java program used to download pubmed is available here: https://github.com/lindenb/jsandbox/blob/master/src/sandbox/PubmedDump.java Note: pubmed contains some errors: e.g. submitted \u0026gt; accepted (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed\u0026amp;id=20591334\u0026amp;retmode=xml) or some dates in the future: ( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed\u0026amp;id=12921703\u0026amp;retmode=xml 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