Scientific Reference managers revisitied.

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Posted by jamesofford
Mar 2, 2009 at 12:24 AM

Some time ago, I posted on my search for a good PDF reference manager for organizing scientific literature. There used to be little in the way of software for this task, but now there seems to be a plethora.

I have ~1700 different papers that I have downloaded as PDF files over the years, and it has been a pain in the ass to keep them in some way that I can find what I want quickly. You could keep them in folders organized by topic or author, which I have done for a while. However, it seemed like this was an ideal job for a computer.

If you didn’t have a large number of files, Endnote worked. You could search, find the reference, store the referene in Endnote with a link to the PDF. Works okay if you don’t have those 1700 PDF files to deal with.

A while back, two programs that claimed to be “The Itunes for references” showed up on the Mac. One is called Papers(http://mekentosj.com/papers/) The second is called iPapers(http://ipapers.sourceforge.net/iPapers.html). I have been using Papers for a while, and it works well. You can import your PDF files, and it tries to parse the metadata to find the author names, journal, title etc and populate fields for each of these so that you can easily store and sort your PDFs. The matching works okay but can be a bit cantankerous. There are lots of other things that it does, searches, smart collections and the like.

There is a new kid on the block, and it has Windows XP, Mac, and Linux versions. It can store PDF files on the web, and you can synchronize across different computers. It even has a “Social Networking” component. This program is called Mendeley(http://www.mendeley.com/) It is a beta, and I have been having trouble with importing my PDF files.

Finally, there is Zotero.(http://www.zotero.org/) Zotero is web based, and started off life as a program like Endnote. Apparently, the latest version does PDF metadata matching so you can import your library of PDF files. Since it is web based, you can have access to your PDF files anywhere you go. I believe that it is also only usable in Firefox, but it works on any computer that has Firefox. I may give Zotero a try.

There is also another Mac program that I haven’t tried, but supposedly does metadata matching. It’s called Sente(http://www.thirdstreetsoftware.com/site/introduction.html)

Nice to see such a great response to a difficult problem.

—
jim offord

Posted by Tom S.
Mar 2, 2009 at 02:26 AM

Jim wrote:

>Finally, there is
>Zotero.(http://www.zotero.org/) Zotero is web based, and started off life as a
>program like Endnote. Apparently, the latest version does PDF metadata matching so
>you can import your library of PDF files. Since it is web based, you can have access to
>your PDF files anywhere you go. I believe that it is also only usable in Firefox, but it
>works on any computer that has Firefox. I may give Zotero a try.

Jim,

Just FYI, be sure to use the new beta (v1.5b1) instead of the older versions. This version has syncing over the net (older versions do not). I’ve been using it since it was in alpha and haven’t had any problems. I don’t have anywhere near 1700 references, though. :)

Good luck,

Tom S.

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