January 18, 2013

How to export, delete and move your Mendeley account and library #mendelete


Delete. Creative Commons licensed picture by Vitor Sá – Virgu via Flickr.com

News that Reed Elsevier is in talks to buy Mendeley.com will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1,2], so it will be interesting to see how this plays out.

If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your mendeley account (aka #mendelete), just that if you do decide to, here’s how to do it, and some alternatives to consider. Update April 2013, it wasn’t just a rumour.

Exporting your Mendeley library

Open up Mendeley Desktop, on the File menu select Export. You have a choice of three export formats:

  1. BibTeX (*.bib)
  2. RIS – Research Information Systems (*.ris)
  3. EndNote XML (*.xml)

It is probably best to create a backup in all three formats just in case as this will give you more options for importing into whatever you replace Mendeley with. Another possibility is to use the Mendeley API to export your data which will give you more control over how and what you export, or trawl through the Mendeley forums for alternatives. [update: see also comments below from William Gunn on exporting via your local SQLite cache]

Deleting your Mendeley account #mendelete

Login to Mendeley.com, click on the My Account button (top right), Select Account details from the drop down menu and scroll down to the bottom of the page and click on the link delete your account. You’ll be see a message We’re sorry you want to go, but if you must… which you can either cancel or select Delete my account and all my data. [update] To completely delete your account you’ll need to send an email to privacy at mendeley dot com. (Thanks P.Chris for pointing this out in the comments below)

Alternatives to Mendeley

Once you have exported your data, you’ll need an alternative to import your data into. Fortunately, there are quite a few to choose from [3], some of which are shown in the list below. This is not a comprehensive list, so please add suggestions below in the comments if I missed any obvious ones. Wikipedia has an extensive article which compares all the different reference management software which is quite handy (if slightly bewildering). Otherwise you might consider trying the following software:

One last alternative, if you are fed up with trying to manage all those clunky pdf files, you could just switch to Google Scholar which is getting better all the time. If you decide that Mendeley isn’t your cup of tea, now might be a good time to investigate some alternatives, there are plenty of good candidates to choose from. But beware, you may run from the arms of one large publisher (Elsevier) into the arms of another (Springer or Macmillan which own Papers and ReadCube respectively).


  1. Whitfield, J. (2012). Elsevier boycott gathers pace Nature DOI: 10.1038/nature.2012.10010
  2. Van Noorden, R. (2013). Mathematicians aim to take publishers out of publishing Nature DOI: 10.1038/nature.2013.12243
  3. Hull, D., Pettifer, S., & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204
  4. Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2010). Utopia documents: linking scholarly literature with research data Bioinformatics, 26 (18) DOI: 10.1093/bioinformatics/btq383

June 22, 2010

Impact Factor Boxing 2010

Golden Gloves Prelim Bouts by Kate Gardiner[This post is part of an ongoing series about impact factors. See this post for the latest impact factors published in 2012.]

Roll up, roll up, ladies and gentlemen, Impact Factor Boxing is here again. As with last year (2009), the metrics used in this combat sport are already a year out of date. But this doesn’t stop many people from writing about impact factors and it’s been an interesting year [1] for the metrics used by many to judge the relative value of scientific work. The Public Library of Science (PLoS) launched their article level metrics within the last year following the example of BioMedCentral’s “most viewed” articles feature. Next to these new style metrics, the traditional impact factors live on, despite their limitations. Critics like Harold Varmus have recently pointed out that (quote):

“The impact factor is a completely flawed metric and it’s a source of a lot of unhappiness in the scientific community. Evaluating someone’s scientific productivity by looking at the number of papers they published in journals with impact factors over a certain level is poisonous to the system. A couple of folks are acting as gatekeepers to the distribution of information, and this is a very bad system. It really slows progress by keeping ideas and experiments out of the public domain until reviewers have been satisfied and authors are allowed to get their paper into the journal that they feel will advance their career.”

To be fair though, it’s not the metric that is flawed, more the way it is used (and abused) – a subject covered in much detail in a special issue of Nature at http://nature.com/metrics [2,3,4,5]. It’s much harder than it should be to get hold of these metrics, so I’ve reproduced some data below (fair use? I don’t know I am not a lawyer…) to minimise the considerable frustrations of using Journal Citation Reports (JCR).

Love them, loathe them, use them, abuse them, ignore them or obsess over them … here’s a small selection of the 7347 journals that are tracked in JCR  ordered by increasing impact.

Journal Title 2009 data from isiknowledge.com/JCR Eigenfactor™ Metrics
Total Cites Impact Factor 5-Year Impact Factor Immediacy Index Articles Cited Half-life Eigenfactor™  Score Article Influence™ Score
RSC Integrative Biology 34 0.596 57 0.00000
Communications of the ACM 13853 2.346 3.050 0.350 177 >10.0 0.01411 0.866
IEEE Intelligent Systems 2214 3.144 3.594 0.333 33 6.5 0.00447 0.763
Journal of Web Semantics 651 3.412 0.107 28 4.6 0.00222
BMC Bionformatics 10850 3.428 4.108 0.581 651 3.4 0.07335 1.516
Journal of Molecular Biology 69710 3.871 4.303 0.993 916 9.2 0.21679 2.051
Journal of Chemical Information and Modeling 8973 3.882 3.631 0.695 266 5.9 0.01943 0.772
Journal of the American Medical Informatics Association (JAMIA) 4183 3.974 5.199 0.705 105 5.7 0.01366 1.585
PLoS ONE 20466 4.351 4.383 0.582 4263 1.7 0.16373 1.918
OUP Bioinformatics 36932 4.926 6.271 0.733 677 5.2 0.16661 2.370
Biochemical Journal 50632 5.155 4.365 1.262 455 >10.0 0.10896 1.787
BMC Biology 1152 5.636 0.702 84 2.7 0.00997
PLoS Computational Biology 4674 5.759 6.429 0.786 365 2.5 0.04369 3.080
Genome Biology 12688 6.626 7.593 1.075 186 4.8 0.08005 3.586
Trends in Biotechnology 8118 6.909 8.588 1.407 81 6.4 0.02402 2.665
Briefings in Bioinformatics 2898 7.329 16.146 1.109 55 5.3 0.01928 5.887
Nucleic Acids Research 95799 7.479 7.279 1.635 1070 6.5 0.37108 2.963
PNAS 451386 9.432 10.312 1.805 3765 7.6 1.68111 4.857
PLoS Biology 15699 12.916 14.798 2.692 195 3.5 0.17630 8.623
Nature Biotechnology 31564 29.495 27.620 5.408 103 5.7 0.14503 11.803
Science 444643 29.747 31.052 6.531 897 8.8 1.52580 16.570
Cell 153972 31.152 32.628 6.825 359 8.7 0.70117 20.150
Nature 483039 34.480 32.906 8.209 866 8.9 1.74951 18.054
New England Journal of Medicine 216752 47.050 51.410 14.557 352 7.5 0.67401 19.870

Maybe next year Thomson Reuters, who publish this data, could start attaching large government health warnings (like on cigarette packets) and long disclaimers to this data? WARNING: Abusing these figures can seriously damage your Science – you have been warned!


  1. Rizkallah, J., & Sin, D. (2010). Integrative Approach to Quality Assessment of Medical Journals Using Impact Factor, Eigenfactor, and Article Influence Scores PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010204
  2. Abbott, A., Cyranoski, D., Jones, N., Maher, B., Schiermeier, Q., & Van Noorden, R. (2010). Metrics: Do metrics matter? Nature, 465 (7300), 860-862 DOI: 10.1038/465860a
  3. Van Noorden, R. (2010). Metrics: A profusion of measures Nature, 465 (7300), 864-866 DOI: 10.1038/465864a
  4. Braun, T., Osterloh, M., West, J., Rohn, J., Pendlebury, D., Bergstrom, C., & Frey, B. (2010). How to improve the use of metrics Nature, 465 (7300), 870-872 DOI: 10.1038/465870a
  5. Lane, J. (2010). Let’s make science metrics more scientific Nature, 464 (7288), 488-489 DOI: 10.1038/464488a

[Creative Commons licensed picture of Golden Gloves Prelim Bouts by Kate Gardiner ]

June 20, 2008

A Brief Review of RefWorks

Philosophiæ Naturalis Principia MathematicaThere is no shortage of bibliographic management tools out there, which ultimately aim to save your time managing the papers and books in your personal library. I’ve just been to a demo and sales pitch for one of them, a tool called RefWorks. Refworks claims to be “an online research management, writing and collaboration tool — designed to help researchers easily gather, manage, store and share all types of information, as well as generate citations and bibliographies”. It looks like a pretty good tool, similar to the likes of EndNote but with more web-based features that are common with Citeulike and Connotea. Here are some ultra-brief notes. RefWorks in five minutes, the good, the bad and the ugly.

The Good…

Refworks finer features

  • Refworks is web based, you can use it from any computer with an internet connection, without having to install any software. Platform independent, Mac, Windows, Linux, Blackberry, iPhone, Woteva. This feature is becoming increasingly common, see Martin Fenner’s Online reference managers, not quite there yet article at Nature Network.
  • Share selected references and bibliographies on the Web via RefShare
  • It imports and exports all the things you would expect, Endnote (definitely), XML, Feeds (RSS), flat files, BibTeX (check?), RIS (check?) and several others via the screenscraping tool RefGrab-It
  • Interfaces with PubMed and Scopus (and many other databases) closely, e.g. you can search these directly from your RefWorks library. You can also export from Scopus to Refworks…
  • Not part of the Reed-Elsevier global empire (yet), currently part of ProQuest, based in California.
  • Free 30 day trial is available
  • Just like EndNote, it can be closely integrated with Microsoft Word, to cite-while-you-write


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