Wednesday, February 06, 2008

Strategies for organizing literature

Newton once wrote to Hooke: "If I have seen further it is by standing on the shoulders of giants". It's true nowdays more than ever, and since there's such a huge volume of literature that is electronically searchable, the hard part isn't finding previous work, but remembering where you have found it.

Here's the strategy I use, which relies mainly on CiteULike and Google Desktop, what are some others?

  • Use Slogger and "Save As" to save every webpage and pdf I look at, put the pdf's online for ease of access and sharing.
  • For more important papers, add an entry to CiteULike with a small comment
  • When common themes emerge (like resistance networks or self-avoiding walk trees), go over papers in that area and make sure they share a tag or group of tags
  • For papers that are revisited, use "Notes" section for that paper in CiteULike to save page numbers of every important formula or statement in the paper.
  • Finally, once a particular theme comes up often enough, review all the papers in that topic, write a mini-summary, put it in the "Notes" section of the oldest paper in that category

I do similar thing with books, in addition to scanning every technical book that I spend more than a couple of hours reading. With double-sided scans, you can average 4 seconds per page, so well worth the time investment. In addition, book scanning has a kind of meditation effect.

To find some result, ideally I remember the author or tag you put it under, then I use CiteULike search feature. If that fails, use Google Desktop to search through pdf's and web history.

What strategy do you use?


Zeppe said...

Mostly CiteULike, for the most important papers, basically. The less important ones I don't track, it would be too much time spent in trying figuring out why did I save them than the advantage in doing that :)

Anonymous said...

I use mindmapping software, which forces me to somewhat create a conceptual tree relating the papers. In each leaf of the tree I save the paper, and put some comments.

Steve Lianoglou said...

I've been using Papers to save my papers and take notes on 'em.

It's a Mac-only app, so won't be helpful for everybody, but I'm loving it.

Anonymous said...

I've just recently started using CiteULike with BibDesk and really like the combination. I wrote a post in response to this one over at my blog.

Yaroslav Bulatov said...

Thanks for the tip Mark, I never realized you had a blog, it's sure to make my weekly reading now

nojhan said...

For those who prefer to keep their bibliography on their computers, there is Zotero, a firefox extension:

For those who need a community oriented towards biology, there is Connotea (a free software, on the contrary of CiteULike):

Yaroslav Bulatov said...

Is Open Source the same as free? Both CiteULike and Connotea are hosted by for-profit companies. Most CiteULike internals are closed-source, although parser code can be viewed and contributed to. I just tried loading my Bibtex file into Connotea, but got "The connection to the server was reset" after 3 minutes of waiting, too big perhaps?

nojhan said...

Last time I checked (some months ago), Connotea used a free (as in speech) software (in perl) but keep the database as a property of the nature publishing group. Whereas CiteULike was using a proprietary software, on a proprietary database too.

IMHO, Connotea is far more clear on its terms of use than CiteULike, which we must trust the good will. I'm not sure many peoples wants to contribute to a proprietary software for free, BTW.

Depsite that, I'm using CiteULike, because it have the most interesting network in computer science.

Anonymous said...

I looked into a variety of web-based bibliographic management tools in the past including Connotea, CiteULike and Aigaion. Incidentally, Wikipedia has a good overview of reference managers which I used as a starting point.

Although Connotea code is freely available I couldn't for the life of me get it running on a server. It requires a huge number of perl modules, each with their own idiosyncrasies. If you want to host your own, private bibliography manager I would recommend Aigaion. It's easy to set up and has most of the features you would want from such a system.

If you don't mind others knowing what you have been reading then CiteULike seems the best bet. If you're worried about their service reliability it's not difficult to download a BibTeX version of your bibliography now and then and store it elsewhere.

Yaroslav: have you tried chopping your BibTeX file into smaller pieces and uploading them sequentially?

Yaroslav Bulatov said...

Mark, it would probably work. I got some help from Connotea team, and managed to upload it, the downside is that about 30% of my bibtex records failed to import because some key fields were missing

Anonymous said...


I have found the use of Copernic to be one of the best solution for finding articles/papers in the desktop. It takes much less space than google desktop and provides your with a text version of the pdf once you highlight the file (you have to click through in google desktop)


Unknown said...


What mindmapping software do you use?


Tomasz Malisiewicz said...

I've been using Jabref on my Mac OS X (its a cool Java bibtex manager) to manage my references, and I save all read PDFs into a papers directory. When writing a paper, I don't need to do any more work.

A friend of mine working on his thesis proposal showed it to me and it will be a time saver when writing my thesis.

mbq said...

Give a try to Mendeley

Yaroslav Bulatov said...

Yup, tried it. I was getting Server Errors when I tried to import my 700 citeulike library but the latest attempt worked.

Anonymous said...

In the wake of perusing this sort of blog we simply comprehend the fundamental and four new and huge mold. This blog is giving us the data identified with the look here paris and the various nations. However, it is hard to embrace this sort of form

Belkis Scruggs said...

James Hickey led a quiet life, but he sure made waves in the region. In a very well written essay by an essay writing service, I was impressed to read the many things he accomplished in his 90 years on earth.

draj said...

Excellent machine learning blog,thanks for sharing...
Seo Internship in Bangalore
Smo Internship in Bangalore
Digital Marketing Internship Program in Bangalore