So far, having met with a couple pf researchers, they just use a single word document for writing notes on the research they accumulate and then assemble the paper using those notes - it seems the most simplistic usage for them.

For archival purposes, they also store their research citations in Endnote.

How do you manage your citations and notes on research and use them for writing papers / literature review?

I am always astounded at just how little use academics in particular make of the many amazing tools out there for collating / structuring information. The "giant Word file" approach seems to be very popular. There's certainly a crying need for some kind of info processing tool that isn't as complex as ridiculously over-the-top implementations like Citavi (or even Mendeley), but still allow you to export neatly formatted citations/end-notes etc.

I was briefly enchanted by NOOKstudy, but appalled on more in-depth use to find out that the search tool is a complete heap of cr*p - oh, and if you've annotated PDF files, there's absolutely no way of exporting the annotated PDF itself (although you can export the annotations - to a Word file - which is less than useless if you've simply highlighted specific passages). I attempted to use NOOKstudy to translate an annual report (the side-by-side feature is brilliant), but discovered that the search function simply doesn't work - even worse, doesn't work consistently between the Library view (which will come up with one lot of results) and the Reader view (which comes up with another set of results!). Very depressing, and proof - if any were needed - that it is very specifically targeted at the educational market...

david wrote:

How do you manage your
citations and notes on research and use them for writing papers / literature review?

I think a lot depends on how complex your research/writing project is. Clearly the more complex and bigger the project, the more need for sophisticated solutions. I don't think there is a single tool that does it all and that serves all purposes. Eventually one needs to assemble the assortment of tools that suit the purpose of the given project best.

Here's my work flow (some of these are simultaneous):

- capture website info with Surfulater;
- capture writing ideas in Notes on iPod Touch/iPad, which syncs with Gmail;
- collect references in EndNote and link to PDFs on PC hard drive;
- read and annotate PDFs with PDF XChange Viewer on PC or GoodReader on iPod Touch/iPad;
- copy quotes and notes from PDF and Gmail and paste them into Whizfolders in order to organise them into hierarchical outline; use Whizfolders as main database of ideas and quotes;
- use NVivo for analysing other collected material (text, image, audio, video).
- draft final outlines in Natara Bonsai;
- do the final writing in MS Word.

This is what I've been doing so far, however I'm interested in replacing EndNote with Citavi and introducing Scrivener for Windows between the Bonsai outline and the MS Word as an interim step.

I also use several other software for managing audio files and image files, as well as brainstorming and mindmapping tools. I may also need to use some timelining software and UltraRecall for organising thousands of digital files. So obviously this is for a big project lasting for several years, not just the literature review.

Dr Andus wrote:

- capture website info with Surfulater;
- capture writing ideas in Notes on iPod Touch/iPad, which syncs with Gmail;
- collect references in EndNote and link to PDFs on PC hard drive;
- read and annotate PDFs with PDF XChange Viewer on PC or GoodReader on iPod Touch/iPad;
- copy quotes and notes from PDF and Gmail and paste them into Whizfolders in order to organise them into hierarchical outline; use Whizfolders as main database of ideas and quotes;
- use NVivo for analysing other collected material (text, image, audio, video).
- draft final outlines in Natara Bonsai;
- do the final writing in MS Word.

Dr,

My workflow was* very similar to yours, but I only used two tools in practice: Surfulater for all reference material and Brainstorm for all writing, apart for the final formatting. I made this choice after trying several tools, including Zoot, UltraRecall, Endnote and Maxthink among others; I liked many of them, but most were redundant or even bothersome in my workflow. This included Endnote; it was for me much more convenient to maintain bibliographies in Brainstorm (even though they were in plain text) as I could link them to quotes and reuse them without disturbing the workflow.

Surfulater is focused on capturing and organising web content, so I grabbed most of my references including articles in HTML form, also linking to the PDF versions in my file system. Highlighting and copying content is far more seamless with HTML than PDFs (e.g. no carriage returns to remove), articles can be included in multiple categories as clones or via tags if one prefers. Linking to the original article from other applications, e.g. Word, is easy via the sulkb:// tag, etc.

Brainstorm is excellent for developing textual content bottom-up or top-down complementarily. It also supports cloning (namesakes) and can identify identical text automatically. I note that it now looks rather dated (it started life as a DOS application after all) and it may have some trouble dealing with huge amounts of multi-cross-referenced text, but I have found nothing as powerful. Nevertheless, I'm now using mostly Sense for top-down writing, as it provides a better overview of the content and is actively developed.


*It's been a year since I last did any academic writing, though I should be getting back to it soon.

One man's "ridiculously over-the-top implementation" is another's "just right," I suppose. Citavi integrates several stages of my research-to-writing workflow and eliminates several other separate applications. It captures references as well as any other ref manager; allows me to embed references in multiple places in my own "knowledge tree"; and allows me to create quotations and notes that remain linked to their sources and which can themselves become part of the knowledge tree (one branch of which might be my current project, or one down the line; a single item can exist simultaneously in as many nodes as you like). It also has a nice task manager feature. It is an extraordinarily robust solution and, given its extensive capabilities, remarkably simple to use. If this is the kind of work you need to do, I highly recommend giving it a try. In my years of looking for something like this, nothing has ever come close.

I generally use it for everything up to the writing stage, including pre-writing outlining, with the exception of quick grabs into Evernote. Evernote is great for collecting stuff, but you can't do much with that stuff afterwards, except search it. When I clip something especially important, I generally email it to myself and use gmail + activeinbox + todoist to turn it into a task attached to a project so it will come under my nose when I'm working on that project.

I'm still fiddling around with various writing programs--WritingOutliner, Scrivener for Win, etc. I'll need to make a commitment in May, when I'll be getting back to writing full-time. However, at this point, I'm not sure I need much more than a word-processor once I've organized and outline my notes and quotes in Citavi. More on that piece later....

Cheers,
David

I'm afraid that I am terribly backward when it comes to writing papers. I write longhand for a first draft. When there is a point of information that I need a reference for, I put (REF) in the text. My second draft is on the computer, and I insert all of those (REF) into the text, but I color them red. I then pull out the references that I need, and put them in a folder. As I go through the next draft on the computer, I enter a more normal reference(Usually something like(Donelson, 1987)Finally, I corral all of the references that I am using in Endnote. If I am working with someone else, the Endnote library gets stored on a Sharepoint site. Writing on the computer is done in Word.
Hopelessly inefficient, but I have found that it is much more difficult for me to compose on the computer.

Jim

Jim,

In this as in most matters concerning writing, to each his own. And if it ain't broke, don't fix it. I pulled these old saws out of my UltraRecall adage database....

In my own case, I have always found myself taking notes on legal pads and in the margins of xeroxes and books--and then just being surrounded by piles of this stuff, unable to find what I want, forgetting that half of it ever existed, etc. This is where I saw the opening for digital assistance--and it's certainly been helpful so far.

Cheers,
David

Fair 'nuff, David - it sounds as if you make full use of Citavi's plethora of features, in which case I stand in awe. Certainly Citavi are pointing the way to a form of integrated application that will, I think, become much more common in the near future, especially as we all become more used to doing serious work on various kinds of content management system. I have a strong feeling that we're about to experience a seismic shift in working methodologies - away from single-function applications (sophisticated though they might be) like Word towards multi-functional environments (presaged, perhaps, by Google's short-lived Wave). Citavi is an impressive attempt to create an all-in-one working environment. But I confess I personally still find it a bit "over-the-top" (perhaps because I have a vision of how a truly integrated workplace application should really function - but that's another story). Kudos to you, however!

Cheers,
Bill

Alexander Deliyannis wrote:

Surfulater is focused on capturing and organising web content, so I
grabbed most of my references including articles in HTML form, also linking to the PDF
versions in my file system. Highlighting and copying content is far more seamless
with HTML than PDFs (e.g. no carriage returns to remove), articles can be included in
multiple categories as clones or via tags if one prefers. Linking to the original
article from other applications, e.g. Word, is easy via the sulkb:// tag,
etc.

Interesting point about using HTML versions of articles to avoid the carriage return removal.That's one problem I have with copying from PDFs into Whizfolders.

However, I can't imagine how I could import my existing 1500 references that are all linked to PDFs seamlessly into Surfulater. The EndNote Word add-in is also essential for me for referencing. I do want to move away from EndNote though, as it's a laggard in terms of innovation and I'm still fuming that I had to buy a new upgrade just because I upgraded to Win 7 and Word 2010. Hence I'm eyeing Citavi, though the learning curve has put me off from jumping ship yet.