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As spring rolls into summer, it is time for another appraisal of my digital research ecosystem. For a brief history of my reflections on digital scholarly research, I invite you to take a ride on the Long Road way-back machine circa April 15, 2010, when I first wrote about the elusive quest to close the digital research circle.

Funny how, in that initial post, I thought I was “tantalizingly close” to closing what I called the digital research circle: the ability to gather, curate, annotate, synthesize and cite scholarship without paper using a seamless digital process. More than two years later, I am still close, but now what felt  tantalizing has tilted toward the torturous.

I will not here rehearse my entire research ecosystem which involves Dropbox, Evernote, Scrivener and even Word, although I invite you to read through and comment on my posts on the issue of digital research. Instead, I want to focus again on what should be the very heart of that ecosystem: the reference manager.

Thinking that I might finally close the digital research circle by taking the advice of @Targuman and @history_geek, I decided to give Sente a try. After a bit of fun with Sente, after two weeks I am back to my combined Mendeley/Zotero model. Here is why:

The great strength of Sente is its capacity to gather, which itself is a vital part of the research process. When I experienced the way Sente integrated with the Penn State Library, felt the ease by which I could pull pdf files directly from our huge collection of databases and have Sente parse them quickly according to their bibliographic information and place them at my disposal on my desktop and in a beautiful iPad app, I thought I had died and gone to research heaven. Soon I realized, however, that although it does have a rich and responsive support forum, Sente is missing what both Zotero and Mendeley offer: a robust capacity to share and collaborate with a research community.

Although I am in a humanities discipline, collaboration is becoming an increasingly important part of my academic research. (OK, that came off as a bit too as too cynical – dial the cynicism back a notch or two, but you get the point.) Here is link to a post about how I work with a research assistant to do collaborative research in philosophy – it includes an embedded Prezi as a bonus.

Despite Sente’s excellence at gathering, its limited social capacities, its outmoded ways of integrating with the word processor (using in-text citation tags and the need to initiate scans of the document – as opposed to using Applescripts), its clunky search features, and its brutal lethargy on the iPad app with certain kinds of pdf files led me back to the Mendeley/Zotero model.

In the meantime, I solved a duplicating problem I was having in Mendeley when I stopped having Mendeley sync to a folder in Dropbox and allowed it to sync to a local drive on my various machines. When it comes to organizing pdfs in a social research context, Mendeley is the best. It even allows you, for example, to embed your profile into your blog posts:

Christopher Long is a member of Philosophy on Mendeley.

Mendeley’s capacity to facilitate collaborative research led me to adopt it extensively in my graduate seminar on Aristotle’s De Anima over the spring semester. My graduate students and I shared a collection, and thus were able to refer to the shared highlights, annotations and notes of our various texts together in class. (Above is a picture of me teaching with Mendeley, referring to a document a student had annotated.) Mendeley’s capacities for collaboration enriched our collective research and our seminar discussions throughout the semester.

Mendeley falters, however, at the gathering and the citing phases. They still have not fixed an issue with html code coming into footnotes when using the Chicago Manual of Style Full Note with Bibliography style. Further, the bookmarklet they use to gather document information from the web is … weak: it does not identify bibliographic information on the website and import it directly into Mendeley as Zotero does so beautifully.

Thus, I am forced to continue to use Zotero for the gathering and the citing phases of the process. I really do like Zotero, and especially now that they have a version that stands alone outside of Firefox. But, it does not hold a candle to the pdf managing capacities of Sente or Mendeley.

If, as they say, sometimes you need many sharp tools to get a job done well, still I wish I didn’t need quite so many sharp research tools to close the digital research circle.


  • Mary A. Axford says:

    Have you ever taken a look at ColWiz (” target=”_blank”> ” target=”_blank”>( It was developed at Oxford and seems to have the biggest set of features for a research management tool. I don't do that much research myself, as a librarian, but I do teach useful tools to graduate students and would love to have someone share if they found ColWiz useful or not.

  • Thanks for this suggestion. I am going to check out ColWiz.

  • As noted on Twitter, I do think that heaven will have quite an interesting community…Chesterton alone will be worth it.
    I do not do anything like the collaboration that you do but I know that Sente does allow you to share libraries. Of course each person has to have a paid copy so that is not useful for a graduate seminar. I have also been satisfied with the citation management, but sadly I have not used it all that much because my pubs are behind schedule. This summer I should give it a good workout for that.
    As for the iPad app being slow, I do think it is related to corrupt or difficult PDFs. I do not have as large a library as you but it is very quick on my iPad2 and very responsive even with a large (200pp) PDF with LOTS of annotations.
    All of that being said, I am not pushing Sente over against the others. Like most apps people need to find what works for them. Fortunately we are in a world now where there is more than one word processor and bibliomanager. Sadly for us we still do not have "one system to rule them all."

  • Granting your point about heaven, I took the liberty to edit that little comment out of the original post. (I had said that Sente, like heaven, lacks an interesting community!) No need for me to get into commentary about the population of heaven; I leave that to you biblical scholars. (Now I see you are encouraging me on Twitter to keep it. It is probably best here in the commentary in any case! All in good fun!)
    I never thought you were pushing a particular app and I enjoy our ongoing discussion about this issue. Having played with Sente, I do see now more clearly its real power. On the forums they have a robust discussion about the slow pdf issue, which seems to have to do with pdf files from older journals that are based on bitmapped images as opposed to pdf files that have been created from original digital files.
    In any case, the quest for the single solution continues for me; in the meantime, I wish you well with the workout you will give Sente this summer. I am hoping to give Mendeley a workout myself with an essay I am writing for a conference in Italy this summer.

  • Thanks CPL! Heaven and hell are so alike in so many ways…
    One article is all but complete (final touches and then we will run Sente for citations, I will keep you posted) and another paper to write by mid-July. And of course the book…

  • Hi Christopher,
    Thanks for the great post. As a community liaison with Mendeley, this feedback is really useful.
    Let me take this opportunity to also let you know that we are actively working to improve the citation plugin (which works across all platforms!). As for the citation style issues, this is also being improved upon. We even have a custom style editor in the baking that should be out and about by the end of the summer.
    Our web importer is as good as the websites it's been developed for. In many cases, the website/databases get updated or change some characteristics and the importer needs updating to reflect these changes. This becomes a bit cumbersome as the number of supported databases increases. However, we've been working on our importer and some other methods of gathering research articles into Mendeley Desktop that should please you. These are in the works and will be released soon 🙂
    Thanks again for the feedback and we hope we can only improve your research workflow.

  • Thanks, Ricardo, for the comment. I am very much looking forward to the upcoming releases of Mendeley. One of the things I really appreciate about Mendeley is the lively community of liaisons you have. I have communicated with @mrgunn in the past, and he has been very helpful in suggesting solutions and pointing me in the right direction regarding Mendeley.
    Regarding the importer, I think Zotero has a good model there. When the icon appears in my address bar, I know I have a reference that can be downloaded. If Mendeley had that feature, it would be a step closer and all I would need is the citation issue addressed. I can't believe that is so hard either, I mean the citation pulls in html code, which is odd.
    In any case, it is great to hear that you are working on it. I will be ready to play with it, once it is released.

  • jearuiz01 says:

    the website/databases get updated or change some characteristics and the importer needs updating to reflect these changes.

  • rickla says:

    Thanks for the post. I pretty much settled on Sente a year or two ago and have surprised myself by sticking with it and not being too tempted by any of the other applications for which I also have licences. My feelings on Sente's strengths and weakness are a little different from yours:
    1. As Christian mentioned above, it's actually one of the stronger applications for sharing (though having to buy multiple licences could be a problem): you can give a copy of any database to as many people as you like, and once they've installed it it will update itself indefinitely without further intervention. The syncing feature also has an impressive range of options: you can allow people to just read your database, to read and edit existing entries, or to do the above and also add new entries. And where digital rights don't allow you to share attachments, you can exclude those from sharing/syncing.
    2. Related to the above, it's the only offering that, in my opinion, offers a good integrated system involving seamless syncing between Mac(s) and iPad(s). (I don't think much of the Mendeley iPad app in comparison.) I have well over 3000 PDFs in my library and the iPad app has recently started to slow down a bit, but until recently I didn't really have any problems.
    3. The annotation system is in my opinion excellent. You can quote text by simply selecting it, and it gives you title and comment fields for each quote. Each note can be embedded in the PDF and in addition saved as text. If you take extensive notes on a PDF on first reading, on subsequent readings you can just refer to your notes and never look at the PDF again.
    4. Unlike you, I find support on the forums poor. However, in the past when I had a major problem and contacted the developers by email, the response was rapid.
    5. There are some weird gaps in basic functionality. For example, they still don't seem to have realised that an edited volume and a simple chapter in an edited volume should not be treated in the same way in APA 6 format.
    Those first 3 points are the killers for me so I'm happy to put up with other problems. It should also be noted that the coming Sync2 is set to make the syncing features even easier to use:

  • This is a very helpful comment, rickla. In the meantime, I have returned more wholly to Zotero:
    I need to write an updated post about my workflow now that ZotPad is working well for me.

  • GBH says:

    Regarding Cowiz I have now down loaded it, but not put anything into it. I will work with it for a while, but I will say that the way in which they push Facebook as a way to connect is very off putting. I have a Facebook account, for my sins, but I would never use it to coordinate research. Way too much intrusive data mining.

  • joeranb says:

    I am one of the founders of Docear, which is a new software for organizing, creating, and discovering academic literature. Today, we released version 1.0 of Docear after a ~2 year beta phase. If you are interested in reference management, you might want to have a look at Docear. The three most distinct features of Docear are:

    1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, … and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).

    2. A ‘literature suite concept’ that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.

    3. A research paper recommender system that allows you to discover new academic literature.

    And Docear is free and open source and available for Windows, Mac, and Linux. More information can be found in our Blog, including a detailed explanation of what makes Docear superior to Mendeley, Zotero, etc. (at least in our opinion 🙂 ).

    If you don’t like reading, there is also a 6 minute introduction video on our homepage 😉

    In case you are using a BibTeX based reference manager such as JabRef (and you don’t want to switch to Docear), you might still be interested in Docear4Word Docear4Word allows you to insert references and bibliographies from BibTeX files to MS-Word documents. Hence, it makes writing papers much easier, since e.g. JabRef has no own MS Word add-on.

    Finally, I would like to point you to a recent Blog post I wrote about what makes an evil reference manager. Maybe the post helps you deciding which reference manager to use (even if it’s not Docear).

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