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

December 11, 2009

The Semantic Biochemical Journal experiment

utopian documentsThere is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses:

  • Blogs for biomedical science
  • Biomedical Ontologies – OBO etc
  • Project Prospect and the Royal Society of Chemistry
  • The Chemspider Journal of Chemistry
  • The FEBS Letters experiment
  • PubMedCentral and BioLit [2]
  • Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3]
  • The Elsevier Grand Challenge [4]
  • Liquid Publications
  • The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it?
  • The Semantic Biochemical Journal project with Utopia Documents [5]

The review asks what advances these projects have made  and what obstacles to progress still exist. It’s an entertaining tour, dotted with enlightening observations on what is broken in scientific publishing and some of the solutions involving various kinds of semantics.

One conclusion made is that many of the experiments described above are expensive and difficult, but that the costs of not improving scientific publishing with various kinds of semantic markup is high, or as the authors put it:

“If the cost of semantic publishing seems high, then we also need to ask, what is the price of not doing it? From the results of the experiments we have seen to date, there is clearly a need to move forward and still a great deal of scope to innovate. If we fail to move forward in a collaborative way, if we fail to engage the key players, the price will be high. We will continue to bury scientific knowledge, as we routinely do now, in static, unconnected journal articles; to sequester fragments of that knowledge in disparate databases that are largely inaccessible from journal pages; to further waste countless hours of scientists’ time either repeating experiments they didn’t know had been performed before, or worse, trying to verify facts they didn’t know had been shown to be false. In short, we will continue to fail to get the most from our literature, we will continue to fail to know what we know, and will continue to do science a considerable disservice.”

It’s well worth reading the review, and downloading the Utopia software to experience all of the interactive features demonstrated in this special issue, especially the animated molecular viewers and sequence alignments.

Enjoy… the Utopia team would be interested to know what people think, see commentary on friendfeed,  the digital curation blog and youtube video below for more information.


  1. Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009). Calling International Rescue: knowledge lost in literature and data landslide! Biochemical Journal, 424 (3), 317-333 DOI: 10.1042/BJ20091474
  2. Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008). BioLit: integrating biological literature with databases Nucleic Acids Research, 36 (Web Server) DOI: 10.1093/nar/gkn317
  3. Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009). Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article PLoS Computational Biology, 5 (4) DOI: 10.1371/journal.pcbi.1000361
  4. Pafilis, E., O’Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009). Reflect: augmented browsing for the life scientist Nature Biotechnology, 27 (6), 508-510 DOI: 10.1038/nbt0609-508
  5. Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009). Visualising biological data: a semantic approach to tool and database integration BMC Bioinformatics, 10 (Suppl 6) DOI: 10.1186/1471-2105-10-S6-S19

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