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Closing the Digital Research Circle

I have been looking for a way to close the circle of my digital academic research. The idea is to do rigorous philosophical research without paper, taking full advantage of cloud computing, the syncing of notes, articles, bibliographic information, and the ultimate production of academic work in a completely digital environment.

I took a decisive step in this direction when I adopted Zotero as my main bibliographic tool. Still, Zotero is bibliography software, and it does not facilitate the reading, note taking and organization of articles and books digitally on mobile devices.

Now, however, with the iPad, I am tantalizingly close to a process that closes the research circle. The problem is that there is no Zotero or Endnote for the iPad…yet. Even so, such bibliographic programs would need to add the functionality of PDF file and ebook reading and organization.

If they did, the research circle I envision might look like this:

Online library research would be directly downloaded as PDF files or ebooks into my bibliography database. It would sync with an app on the iPad and iPhone where I would easily read the text, annotate it, take notes, etc., all of which would stay with the digital article/book and it’s bibliographic information. When I begin to synthesize my research, I would be able to search all my notes, which should be organizable via tagging. As I write, I should be able to pull the bibliographic information into my word processor, refer easily to my notes, pull up articles and books, and continue the circle of research and writing.


  • Sebastian says:

    Even so, such bibliographic programs would need to add the functionality of PDF file and ebook reading and organization.

    this of course goes both ways – if apple had decided to have FF run on the ipad Zotero would already work with it. I think we’ll pretty soon have readers/tablets with full OS functionality that will take care of this.

  • Christopher P. Long says:

    I agree that allowing FF to run on the iPad/iPhone platform would be an improvement and I take your point about functionality going both ways.
    It was good to see Opera approved as an iPhone app, so perhaps we will see FF there too.
    However, even a fully functioning Zotero through FF on the iPad or any tablet device would not be designed to facilitate really active reading of documents on the tablet. This is what I really need to close my circle.


    This is a nut I have been trying to crack for a while now. I have not been able to get behind Zotero because it is browser based and can only be installed in FF. That just does not work for me.
    Currently, I subscribe to RSS feeds for journals and searches via Google Reader, click through to things I am interested in and then use a bookmarklet to open them in Papers. Then I can read and annotate and all that stays embedded (and searchable) in the PDF. Then I build a smart list (based on tags) in Papers that has all my references for a particular paper. I can then export them to Endnote and use that along with Pages for writing my articles. Still not as friction free as I would like, but I strive onward toward that sunny utopia where everything will get done for me.


    Ah, forgot one thing. Papers on iPad will sync to Papers on my Mac, so all the PDFs in any smart group i set get transferred to my iPad for reading. The annotation on the iPad is not as useful as on the Mac, but at least I can read.

  • Mr. Gunn says:

    Hi Christopher! There are plans for making Mendeley available on mobile devices, as since we’re already cross-platform on computers, you can expect that we’ll work on the ipad as well as android-powered devices.
    It’s truly a challenge to support all the varied ways people work and write, but we hope we can give you the flexibility to finally close the loop.
    Please don’t hesitate to email if you want to know more.

  • Here are what I am doing:
    1) Use Zotero to keep all references and PDF files on my main laptop (needs FF)
    2)Change the PDF file names using the “Rename file from Parent Metadata” function
    3)Convert selected PDF files into Word documents using ABBYY FineReader or ABBYY PDF Transformer. (These ABBYY products are amazing in converting PDFs to Word docs.)
    4)Import all the documents to NVivo, which is an excellent qualitative research tool
    5)Log on to the the main laptop from anywhere by using any device that has a remote desktop feature (I know that iPad also has several apps that allow you to do this)
    6)Start annotating, categorizing, and classifying the content.
    –> You can keep everything on one computer and annotate documents using NVivo. Your synthesis work becomes a lot easier this way, although it requires some conversion work.

  • Christopher P. Long says:

    Yikes, Hyung, that seems like a lot of steps to go through to do some annotating. I think things are getting easier as Dropbox and the iPad are playing well together. Also, Mendeley does a nice job of handling the renaming of PDF files if you tell it how you want to format the names.

  • I did not know about Mendeley, but I’ve tried it upon your suggestion. It is a great tool! I would say that Mendeley is a combination of Zotero and PDF Reader, which are good for reference management plus annotation. Also, I found that Mendeley is great for sharing documents among a private group. As far as I know, Zotero does not allow a group to share actual files. Although I heavily rely on Zotero, I see myself using Mendeley for group projects.
    I believe that using NVivo is a different story as it is a serious qualitative research tool. Like your reaction, I would not use NVivo to review and annotate a small number of documents as it involves multiple steps. However, if you need to analyze and synthesize approximately 10 or more articles or scripts, perhaps NVivo would be the most effective tool. I know that the developer (QSR) of NVivo is trying to make this process simpler.

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