Integrating Mendeley into the Research Circle




Mendeley

Originally uploaded by AJC1

It seems that my quest to close the digital research circle has been joined by a few fellow researchers. 

The idea is compelling and would not only save both time and paper, but would offer new opportunities for collaborative research.  
In my post, Closing the Digital Research Circle, I outlined the basic structure by which we could download PDF files into a reference management system that would handle bibliographic data and manage the PDF files themselves. These libraries of files and data would be sharable with others, or made private. Notes could be take digitally, the files could be annotated and remained synced in the cloud so they are accessible across multiple devices. Finally, the bibliographical information would interface seamlessly with word processing programs so that the transition from gathering to integrating to processing research and, ultimately, to creating new work could be done dynamically and digitally.
In the weeks since I wrote the post on Closing the Digital Research Circle, and the follow-up post, Zotero, the iPad and Summer Research, I have started to play with Mendeley

Mendeley is being designed and developed by the people who made Last.fm, and the idea is to do for research what Last.fm did for music. What they have done for me, though, is offer an easy way to organize all my pdf files with their bibliographical information. They have also given me an easy way to create a digital vita with links to pdf files of my work accessible to those who visit my Mendeley Profile.
Mendeley has both a web interface and a client. Applications for the iPad, iPhone and Droid are being developed, at least according to William Gunn, who has been very helpful in introducing Mendeley to me. Having played a bit with Papers, Mendeley has much of the same file managing functionality and the same iTunes-like ease of use, but adds the dimension of bibliographic information and the ability to share libraries on the web.
The benefit of Mendeley over Zotero is that Mendeley also gives you the ability to annotate PDF files right in the program itself. The social side of it is also more dynamic than Zotero. The strength of Zotero over Mendeley is its ability to simply bring bibliographical information from the web via the Firefox web plug-in into your library.  Zotero does this beautifully. Happily, Mendeley integrates well with Zotero and you can have your Zotero library sync with Mendeley.
So, we are now getting closer to the ultimate vision (although I am still thinking about how best to integrate ebooks into the process, but one thing at a time). Here is what I do now:

    1. Download bibliographic information and pdf files into my Zotero library using the Zotero Firefox plug-in.
    2. Sync with Mendeley to bring the Zotero information and the files into Mendeley.
    3. Have Mendeley organize my pdf files to a folder on Dropbox.
    4. Using the iPad Dropbox application, connect to the folder into which Mendeley has organized my files.
    5. Pull up the paper, read it in Dropbox without annotation, OR
    6. Using the Open In button at the top right, open the file in iAnnotate for the iPad and do annotations right there.
    7. Sadly, to return the document to Dropbox, you will need to email it back to yourself and overwrite the file in Dropbox – this is the weak link at the moment.

      So, we are getting closer here. I am very hopeful that a Mendeley iPad application will have adequate annotating capabilities and file managing abilities, but until then, this just might work for me. 

      Join the discussion 12 Comments

      • Mr. Gunn says:

        Thanks, Chris. We’ll keep working to close the loop. The idea is indeed that your annotations should sync across all platforms as well, so you’ll always have what you need without having to leave the app.

      • Mr. Gunn says:

        Thanks, Chris. We’ll keep working to close the loop. The idea is indeed that your annotations should sync across all platforms as well, so you’ll always have what you need without having to leave the app.

      • Christopher P. Long says:

        Thanks, William, for responding. I am really looking forward to seeing the new mobile apps from Mendeley when they come out. To have everything in one place would be a huge advantage.

      • Tom Benson says:

        Chris, this is an interesting thread — and project — and I hope you will press on with it.
        The iPad is tantalizing and frustrating for just the reasons you describe — it does so many things well, but makes it hard to work across applications and documents.
        Have you tried Evernote for web capture and note-taking? It does at least address some of the problems you describe, but even it is hobbled on the iPad, as it is not possible to clip to Evernote directly from an open web page. But it is possible to copy and paste.
        See also Ann Kirschner, “My iPad Day,” Chronicle Review, June 13, 2010.
        http://chronicle.com/article/My-iPad-Day/65839/#top

      • Christian says:

        “The strength of Zotero over Mendeley is its ability to simply bring bibliographical information from the web via the Firefox web plug-in into your library.”
        You can do this too in Mendeley: http://www.mendeley.com/import/

      • Thanks, Tom, for reading and taking the time to comment. I agree about the tantalizing dimension of the iPad: it is excellent in many ways, but hobbled in others.
        Evernote is an integral part of my daily workflow. I use it for all my work related note taking and increasingly for scholarly work too. The advantage is that I have my notes up-to-date across all devices and platforms. I don’t use the web-clipping feature as much as I might, and I can understand how it is frustrating not to have it on the iPad.
        I would love to see Evernote as a plug-in for Mendeley or for Mendeley to offer similar functionality to their mobile and desktop apps. The former would be better for me as I already have so much on Evernote.

      • Christoph says:

        Hello,
        I really enjoyed this article. I am trying to integrate the iPad into my own workflow, but the dropbox integration is still wanting. One project that might help you get around at least some of the hassle of putting the PDFs back into dropbox is a new service called Habilis, that lets you send files to your dropbox via email. Not quite there yet ( you cannot set folders, for example), but it is certainly a start.
        Check it out:
        http://www.gethabilis.com/

      • I did an interview with NPR on Reading Dickens Four Ways….which became Reading Dickens FIVE ways with the introduction of the iPad.
        http://kirschner.org

      • Kurt says:

        Great post, Chris. Thanks for the introduction to Mendeley. I’ve been a very happy Zotero user, but Mendeley has some great features missing in Zotero:
        1. “PDF renaming and filing: Mendeley can rename PDFs based on bibliographic data, e.g. “Author – Year – Title.pd” …”
        This alone is brilliant. I spend a lot of time renaming every new PDF with a similar convention.
        2. “Citation extraction: Just drag & drop PDFs into Mendeley Desktop to start the automatic extraction of bibliographic metadata (authors, year, journal, volume, issue, etc.)…”
        Again: Excellent. And if the XMP metadata isn’t embedded in the PDF, Mendeley tries to get the metadata by scanning the full-text. Wow. I’d be interested to see how well this works. For instance, how would it know how to parse out authors first and last names, much less find them in the first place.
        3. “Research database lookup: Mendeley cross-checks your research paper collection against external databases like CrossRef, PubMed, arXiv, or Google Scholar, using DOIs and other unique identifiers. When additional information, such as abstracts and keywords, are available, they are automatically added to your research paper library.”
        Great feature. I’m don’t think Zotero has this.
        Although the Mendeley website doesn’t say this explicitly, I assume your library and files are stored in the cloud so they’re accessible from any computer? If so, how much storage do you have? Are there costs for more storage? The one thing I love about Zotero is it’s entirely web-based; no need to installed an “i-Tunes” like program on your PC. Is Mendeley similar in this regard?
        And GoodReader’s PDF reading features are lightyears better than Dropbox’s, so immediate integration with GoodReader would be great (although GoodReader can download files from Dropbox, but that’s one more step and it creates yet another copy of your PDF). As for emailing files to your Dropbox, I’ve been happy with http://sendtodropbox.com/. You just email the PDF to the email assigned to you (add it your contacts and call it “Dropbox) and it shows up in Dropbox seconds later, in a folder called “Attachments.”

      • Christopher P. Long says:

        Thanks, Kurt, for this comment. I agree with you that Mendeley seems to have surpassed Zotero in feature sets.
        Yes, your library in Mendeley is stored in the cloud and you can access it on multiple devices, including now, their new iPhone app. You get 1 GB of storage for free, 500 MB of it is for personal space and 500 MB for shared libraries. They have more options if you are willing to pay a bit.
        They are developing an iPad app, which I hope will deal with the question of annotating pdf files. Mendeley can be used from the web interface, although I think the integration with word processing is handled by the desktop app (unlike Zotero, which handles it all through Firefox.)
        I will have to look into sendtodropbox, but thanks for the tip! I will be interested to hear if you decide to move over the Mendeley from Zotero.

      • AW says:

        You and I are on the same page in many ways. I find, though, that the care and feeding of Mendeley is not delivering in the long run, so I ditched it. Love your blog.
        http://bit.ly/9VzZ3w

      • And GoodReader’s PDF reading features are lightyears better than Dropbox’s, so immediate integration with GoodReader would be great (although GoodReader can download files from Dropbox??

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