Downloading and Installing PubCrawler (version 2.40)


Starting from version 1.80 there will be no specially packed version for Macs or Windows anymore, only the script itself and a sample configuration file.


  • Perl program: (178 KBytes)
  • sample configuration file: pubcrawler.config (13 KBytes)
    Note: Please see --help for new option 'mail_features'!


  • Version 2.40
    date: 2020/05/14
    • updated links to point to new Pubmed URL

  • Version 2.36
    date: 2016/09/22
    • removed links to 10th anniversary
    • allowing fractions for the break between calls
    • added number of total hits to e-mail subject
    • slight adjustment to check for retrieval error
    • switch to use of HTTPS protocol

  • Version 2.16
    date: 2010/07/03 08:24:49
    • changed dispmax for links to NCBI from 500 to 200 (highest number currently accepted)
    • changed output links to avoid double forward slashes
    • includes references to 10th birthday

  • Version 2.15
    date: 2009/05/22 12:55:31
    carry out e-mailing for each address individually to avoid long line of addresses being cut off

  • Version 2.14
    date: 2008/12/09 10:34:37
    parameterization added by David Bistor

  • Version 2.13
    date: 2008/06/26 20:59:13
    more permission changes to avoid problems with WebService

  • Version 2.12
    date: 2008/06/26 20:21:25
    changed permissions of some of the files being created to avoid problems with the WebService which is run under multiple accounts

  • Version 2.11
    date: 2008/06/11 13:13:56
    updated link to WWW-Service and News (now Google Groups)

  • Version 2.10
    date: 2008/06/10 19:02:00
    • avoiding removal of '[All Fields]' in query
    • avoiding putting query into upper case

  • Version 2.9
    date: 2008/05/30 14:29:07
    • adjusted summary link for nucleotide database
    • added new link for retrieval of entries from PubMed
    • made sure that all links are less than 4080 characters long
    • added link_format option, so that hits retrieved through links can be displayed in something other than Abstract Plus

  • Version 2.8
    date: 2007/06/27 09:29:04
    changed backup results file ending from .bak to .bak.html (to enable easier download)

  • Version 2.7
    date: 2007/03/31 19:52:33
    • added AbstractPlus to viewing options
    • removed some of the log messages
    • added 'darwin' to systems (to make it work on Mac OS X Tiger, thanks to David J. Evans for pointing this out)

  • Version 2.6
    date: 2005/11/01 14:54:12
    use collective name if no authors are listed

  • Version 2.5
    date: 2005/10/04 20:40:55
    changed e-mail address to

  • Version 2.4
    date: 2005/09/30 01:15:32
    fixed error introduced through last fix (first author name was not reported)

  • Version 2.3
    date: 2005/09/22 20:30:41
    fixed problem with extracting XML items that are stretching across multiple lines

  • Version 2.2 adjusts the tool to changes in the XML output delivered by the E-utilities (author names and UIDs were not recognized anymore).

  • Version 2.00 uses the new E-utilities provided by PubMed and presents results in a new format.
    Please upgrade if you are still using a 1.x version!

  • Version 1.81 fixes a problem with downloading GenBank entries!

Please report problems to

See the old instructions for more information on installing and running the program.

To receive information about PubCrawler updates, please subscribe to the PubCrawler Mailing List!

For information about how to compose NCBI PubMed and Entrez (GenBank) search queries, see NCBI's detailed description pages or their overview of PubMed.

Note: The first day you run PubCrawler, you will probably get a very large output file with a lot of hits.  You will also get large output files the first time you run it after changing your search criteria.  This is because PubCrawler normally compares the results of today's search to a database listing the PubMed/GenBank entries it has met on previous days, and then only shows you the new ones; but the first time you run a search, all of the "hits" it produces seem new.

Last modified on Fri May 15 08:59:55 IST 2020