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Calculating time from submission to publication / Degree of burden in submitting a paper

posted on 12.10.2012, 10:40 authored by Pierre LindenbaumPierre Lindenbaum, Ryan Delahanty

Inspied by this post on biostar: http://www.biostars.org/post/show/54473/calculating-time-from-submission-to-publication-degree-of-burden-in-submitting-a-paper/ initialy asked by Ryan Delahanty


the script 'pubmed.sh" downloads the the journals from http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.pubmedhelptable45/ , the 'eignefactors'  from http://www.eigenfactor.org

for each journal , It scans pubmed (starting from year=2000) and get the difference between the date(submitted) and the date(accepted). 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 > accepted (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=20591334&retmode=xml) or some dates in the future: ( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12921703&retmode=xml )