The best way to organise ebooks, notes, & references for your PhD

Surely, I do not mean "the" best way. The best way is for you to find out, one and/or the combinations that suits you the most.

Here, I share the best way that works for me- a technological noob on the humanities' side, who doesn't know and doesn't have time to work and think over complex codes that make your work really easy. I'm a lazy bug who for some strange reasons has to complete a humanities thesis in the space of a year. (If you're only looking for the best software to manage your ebooks, close your eyes, and download Calibre. Though with it, as with any other, you have to spend hours attaching tags to the books and files you once stored in different folders. And if you really do have the time to systematise your study, I suggest you can use the quotation manager TextCite, and make a good use of its category functions to organise your reading notes.)

My intention here is different. I am disorganised to the extent that the effort and time that goes into my attempted writing of a PhD dissertation makes it impossible for wander beyond my writing, for the time being, or to systematically organise my ebooks for purposes other than that of writing. So what I tell you here might come of help if you're working against a deadline, and your technological capabilities like mine doesn't go beyond a little typing skills in MS Word.

The sublime object of Bibliography

For some time I have been looking for a way to refer to my modest collection of about 10 GB of ebooks in pdf, html, djvu and other formats; about 5GB of journal articles and randomly scribbled notes in MS Word. And I've been trying to access these for the last two weeks to write a chapter of about 20,000 words, and the footnote entries stand as of now at 178, with a book or an article to cite for most. I had to do this following one of the the humanities styles listed by the Chicago Manual of Style, and I found the manual entering of citations is really a pain in the ass, especially when you've to concentrate on the writing, and at the same time, look for the obscure useless book stored somewhere in your hard drive that you've read and which exists for no worthy purposes beyond the cursory citation. This made me look for two things: a organiser of ebooks and articles that is (and importantly) a bibliographic citation manager. Like an idiot, the first thing I turned to was EndNote.

Managing Citations and the complex world of Citation Managers

After playing with EndNote for a week, I realised this was not for me. It's expensive: from where does a third world 'researcher' procure $ 300, and pay additional shipping charges, apart from the why of it? And perhaps with the reasons to do with its price, EndNote's interface is confusing for the uninitiated (read someone whose university doesn't have a commercial tie-up with the company). Another of my objections is that EndNote created more problems in terms of storage, unless you constantly upgraded your stuff. Even without upgrading, EndNote sucks. For example, if you've a desktop running on Windows XP with Word2003 installed, and a laptop with Windows 7 with Word2007 installed, and use a USB stick between the two for small file transfers, there's no simple way to migrate your bibliographic data, insert and cite (their 'Cite While You Write' function) from the same EndNote file in which you've once stored your citations. And after an endless session of scanning their tutorial videos, their forums, and googling solutions as how to get rid of the "invalid class string" message that appears every time I try to insert a citation from EndNote to Word, I decided that I had enough.

I tried Zotero for a few days, the free and open source add-on for the Firefox browser. While it worked good for synchronising notes taken from the web, there was no going beyond the proverbial Firefox way of crashing. I usually take a long smoking break when my favourite Firefox crashes, but this was a bit more. Zotero crashed everytime I tried to append a pdf ebook to it from my hard discs, and a number of times, without any provocation. I almost got lung cancer!

And for a day and two after that, I tried using Mendeley. As an offline and web-based hybrid citation manager, Mendeley too was free and excellent in terms of its management of books, articles, and citations, and the way it effortlessly scanned my library and fetched names, etc. off the files, and also made the insertion of citations in Word very easy. If you're planning a shorter work (let's say a journal article), Mendeley should be the obvious choice. For longer works though, I'm skeptical about Mendeley on two counts. One, synchronization between the offline version and the online Mendeley account of yours takes hours, especially if you live on slow internet connections in the southern hemisphere. Two, its free online storage capability is only 500 MB (you've to pay to "upgrade" your storage), which plays one of the older tricks of proprietary software industry's money-making.

It was at this point, I was on the verge of frustration, and almost decided to go back to the manual entry process in MS Word. I was and am wary of open source: who doesn't know that what the geeks call "really simple", really requires hours and hours of unfruitful scripting for the technologically incompetent such as me? But I thought I would try at least one. And I'm happy that I did, I found one that didn't make me look back.

I found JabRef . And my ecstatic advice to you: If you're looking for one that makes your work easy, try JabRef- the best bibliography manager for the present. The best thing for JabRef is that it easy for the first-time user and uncomplicated. It takes at the most 10-15 minutes to learn. Moreover, it is consistent than EndNote, or the word citation manager that comes default in MS Word 2007; it is so because the techies say JabRef is based on BibTeX. And finally it always free to try, and improve on (if you are into coding), because it is open source.

How JabRef works

Once you download and install it, you open JabRef, create a database, and click the green (+) sign for a new entry. (BTW, you have to have Java installed on your computer. If you don't have it, get it from here).

There appear simple fields to insert your bibliographical data and linking facilities to either files in your computer or on the web. It's really that simple! And this YouTube video below explains most of the rest:

I found out that I can easily customise on the input fields for the bibliographic entry. And if you require more variations on the Chicago style using JabRef, they don't come by default with the JabRef software. But you can easily download an excellent plug-in (developed by Juan Jose Baldrich) called "Chicago Manual of Style export filters" (check here for the English version). Download the plug-in and install it in the following steps:
JabRef>Plugins> Plugin Manager> Install Plugin
Once you've installed the plug-in, you can export your entire bibliography (or select entries) in a rich text format (.rtf) file that opens in MS Word with your citations arranged according to your preference following the Chicago manual.

Also if you're lazy like me to desire a set of insert buttons in MS Word that automatically insert a citation, or create a bibliography on the document in which you are working, you can do that with JabRef. For that, you just have to install two other pieces of free software: the basic version of a word-processing package called MikTeX (available here) and the Word-integration software called Bibtex4Word (available here). The developer of Bibtex4Word has put up a very comprehensible step-by-step installation instruction here, and you can refer to it if you have problems installing. (As I've found out, with JabRef running, Bibtex4Word works perfectly with Word 2003 and Word 2007). Again the chicago style doesn't come by default, but you can download it (and numerous other sytles) off the MikTeX site by going through the following steps and choosing:
Your Computer's Start Menu>All Programs> MikTeX>Maintenance>Package Manager> chicago or chicago-annote (you find these by scrolling down the entries on the left side of your screen). Select chicago-annote and click the install (+) button.

Once done, you can integrate JabRef with MS Word to seamlessly insert your citations in your manuscript, and to look up ebooks, articles, and links inside the same window. It really saves time; believe me!


Debapriya said...

You are a lifesaver! One of my friends directed me to your post and boy, am i thankful. I haven't tried your suggestions but will asap. Thanks a bunch for sharing this.

Jonathan said...

Yes, Endnote sucks. JabRef is more fun if you are working with LaTeX.

Ankit said...

I should thank the inventors but also much thanks to you for the wonderful info.

After two years with EndNote and its version incompatibilities, I have made the switch to JabRef. And I don't regret it. It happens that I have entered 500 detailed citations in JabRef in three days and still the JabRef file size is so small. Apart from minor errors, the citations work wonderfully in Mikrosoft Word. Suits me fine.

Larry Wyshcroft said...

Great. Calibre works fine.

Anonymous said...

if you like jabref you might be interested in our modified version of jabref. this version is able to extract metadata from PDFs automatically. that means you can drag&drop a PDF to jabref and jabref will extract metadata (title, author, ...) and create a bibtex entry with this metadata automatically. read here for more information:

Joeran (Docear) said...


wir haben heute "Docear4Word" veröffentlicht, ein Add-On um wie mit BibTeX4Word Referenzen in MS Word zu verwalten (basierend auf BibTeX Dateien). Die Nutzung ist wesentlich komfortabler als mit BibTeX4Word und man kann aus über 1700 Zitationsstilen auswählen. Das Add-On ist kostenlos und Open Source. Feedback mit Verbesserungsvorschlägen ist herzlich willkommen (am besten in unserem Forum).


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