Figuring out how to work with mendeley

I am trying out Mendeley and may recommend using Mendeley to my students in my hlth 460 course. However, as with all software, this one too has its share of learning curve. After working with Mendeley, it seems to me that it can not replace Endnote but it might be a good supplement to Endnote in adding some functionalities like web integration but then I have not tried endnote web either in formatting my writing. If endnote web plays well with open office and word, then that might be a better deal. I will also try to use Zotero to see how that works. My only concern with Zotero is that, although it’s a full fledged mozilla app, it still binds itself to firefox and you cannot really use it if you do not have firefox installed. Other than that, it’s a great tool too. But more about that later.

Reflections on Mendeley

Mendeley does have a user manual. The user manual is very basic, just about explains stuff that you can learn pretty much on your own if you play with it for a while.
The way I have seen so far, the workflow is something like this.

Collect stuff off the web (Google scholar, pubmed, others) –> push to either Mendeley or Delicious or Citeulike –> eventually push stuff to Mendeley web collections –> create collections for each project you are working –> push references from the main collections to the subcollections –> tag the articles appropriately –> delete or clean up based on tags (there can be heavy duplicated and mendeley does not yet have the facility to auto detect duplicates like endnote can) –> push them to the desktop client and work off from that. However, at this stage, I might use Mendeley as something that sits between my web readings/offline readings and word processing.

Basically, this what Mendeley can do:

1) As you search the web, it will get the necessary references for you directly to the library
2) It can talk to Citeulike (which in turn can talk to delicious) so you can have all your references stored in citeulike and then from citeulike with mendeley plug in get them to your reference management system

3) Citeulike can also talk with Google reader so with citeulike google reader connection, it is qjuite possible to get everything loaded onto citeulike (ie all journal RSS entries automatically)

Essentially, all journal references and book references and everything gets loaded into Mendeley and then tweak Mendeley to work them around. The way Mendeley does them is as follows:

1) All references are stored in "all references" section
2) There is a subsection of the all references titled "recently added" which really do contain all recently added references
3) That’s about it.

4) Then there are sort of tags called "collections" which can be "created" etc where references can be "moved". I say moved because even after you move something to a collection, the reference stays in both the all reference area as well as the recentlhy added area. Which means, all references are there as one large pile of references which you can use to shift references between one collection and another. Thus collections are just different subject headings or projects in which I am working and I can move or shift references from them as I like. Perhaps after I am done with one of my projects, I can even remove the collection and that’s it.

5) There is a desktop client which syncs with the web version. However, there is a catch. It cannot sync from desktop to the web version, but all changes in web version will be reflected in the desktop version. So, if you have to do any cleanups etc, just do that on the web version not on the desktop version.

6) The desktop version is good at only in transferring data from your mendeley desktop to your word processor of choice, or exporting all references to an RIS file, or bibtex file, etc.
I think this is the reason why I’d still use Mendeley as a reference organizer and limited use as OpenOffice or Word reference insertion (although it’s quite nice that way).

Thus, as long as references can be obtained and archived using the social web and sorted, stored, and manipulated using Mendeley desktop (most grunt work should be done on the Mendeley web), it should work fine.

I think that said, it boils down to this.

1) Read widely. Get on to the web. If it’s a book that’s available on Google Books, use Mendeley to put it on the Mendeley website (then you can tweak the book chapter etc to work it out). If it’s a journal article and Mendeley can read it, all the better. If not, then save it to Delicious and then put it to citeulike. If you are on citeulike or can export it to citeulike, use citeulike. If you are reading an RSS feed on Google Reader or feedly share it to citeulike and from citeulike draw it in to Mendeley.

2) Let Mendeley do the grunt work of formatting references, identifying the PDFs from the web and storing it
3) If you have a PDF, drop it in the Mendeley desktop and let Mendeley figure it out to extract data and list of references

4) At that point you will have a list of references on the all references list box
5) Process that into your project collections
6) Make heavy use of tags to tag and annotate documents
7) Use the tags then to deal with the articles — ie, merge, delete, remove, push to trash, etc

I’d probably still export Mendeley collections as RIS to Endnote to do more stuff that one does with reference collection, but alternatively, one can think of using Mendeley desktop collections for most of the work. However, there is a catch here. You can delete a reference from Mendeley desktop and have no impact on the webtop. But if you delete a reference from webtop, that gets deleted from desktop too when you sync.

"There’s a crack in everything, it’s how the light gets in." (Leonard Cohen)


2 thoughts on “Figuring out how to work with mendeley

  1. Hello,

    if you like mendeley, our software “sciplore mindmapping” might be interesting for you, too. sciplore mindmapping is a mind mapping application that allows you to integrate your pdfs and references with mind maps. the big advantage of this approach is that you do not have only a list of your PDFs but a mind map in which you can add additional information and arrange PDFs more flexible. And in case you really like Mendeley, you can even use Mendeley in addition to SciPlore MindMapping.

    For a short demonstration of sciplore mindmapping see

    To try the software (open source, Java):

    and to read about how to write a phd thesis (or academic papers in general) with sciplore mindmapping see


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