Organizing your PDFs

Remember the days of overflowing file cabinets filled with reprints and photocopied articles? Today many computers are now crammed with article PDFs. Based on what we have heard, many of you are looking for ways to organize your PDF collections so that you can easily find the articles you need. There are a number of software solutions for managing PDFs on your computer, or creating stable links to online articles. Since it is not possible to describe every program or approach, this article gives you a few ideas help you solve this problem. Currently, there are more Macintosh (MAC) than PC applications for this purpose. The web-based tools will, of course, work with either a PC, or a MAC.

Desktop PDF Management Applications

iPapers – (MAC only) iPapers lets you download PDFs from PubMed, and captures the author, journal, abstract and other citation information at the same time. It also lets you add non-PubMed and supplemental items. You can drag and drop existing PDFs into iPapers. Free.

Papers – (MAC only) “Papers” allows you to import, download, organize, and read your PDFs on your computer. PDFs already on your computer may be dragged and dropped into Papers. PubMed and other article search engines can be searched from within Papers, and PDFs can be easily downloaded. Metadata for articles (authors, journal name, etc.) can be obtained from PubMed, Google Scholar, and other sources, and matched with imported PDFs. PDFs can also be organized by subjects (called collections) and additional notes added. Desktop license costs $42.00.

Yep – (MAC only) Think “iTunes for PDFs.” Yep scans your hard drive for PDFs, tagging the ones it finds, or allowing you to create your own tags. Desktop license costs $34.00. (Tip: You can also use iTunes to manage small to medium PDF collections.)

QUOSA – (MAC/PC) You can search PubMed and Google Scholar from within QUOSA and then download the PDFs you want and save them on your computer. You can also export article metadata and links to PDFs to EndNote and other bibliographic management software. For pricing, contact

EndNote – (MAC/PC) Users of the desktop version of EndNote can link to PDFs on their computer, or embed PDFs within the EndNote library. Then you can employ the power of EndNote to search for the references you want, and open the associated PDFs. UCSD Bookstore price is $110 for students, $200 for faculty and staff.

Free Web Tools That Link to Online Content

RefWorks – RefWorks is a web-based tool that is similar to EndNote. Refworks allows you to store documents including PDFs, up to 100 MB per account (EndNote Web does not permit the storing of PDFs and other files). Free for UCSD faculty, staff and students.

CiteULike – CiteULike helps you organize and share the scholarly papers you are reading. When you see a paper on the web that interests you, you can automatically add the reference to your personal library, with the link to the online article retained. You can also upload the PDF, if you have it. It all works from within your web browser and your references and PDFs are stored on the CiteULike server, so there is no need to install any software. CiteULike references also include the orange UCeLinks icons that allow you to link to the online article if UCSD subscribes, check to see if the article is in one of the UCSD Libraries, or order it on interlibrary loan.

Connotea – Connotea allows you to save links to any page on the web. On certain sites, including PubMed and many journals, Connotea recognizes the citation details and saves them for you. Even if Connotea does not automatically import bibliographic information for all the websites you use, you can still save and share links to those pages. You can also assign tags to your entries, see what others have added to Connotea, search part or all of Connotea, and see related articles. References include UC-eLinks links.

Zotero – Zotero is a Firefox extension that helps you gather, store, and organize citations, PDFs, web pages, images, etc. It automatically stores author, title, and publication information and lets you export that information as formatted references. It also allows you to easily save PDFs to your computer. Zotero runs on your personal computer and works with Microsoft Word. It can be used offline as well (e.g., on a plane, in an archive without WiFi). In 2008, Zotero users will be able to share their collections through an exchange server, and receive recommendations and feeds of new resources that might be of interest to them. People considering EndNote or RefWorks might want to consider Zotero, a robust tool with many features.

Categories: Tech Tools Comments: 4

4 comments for “Organizing your PDFs”

On May 26, 2008, 12:57 AM Alethea said:

Are there any equivalents to Yep for PC users? I have a large archive of already-downloaded PDFs and would like to not have to manually tag them, nor re-download them each time I want to read something. I will give it a shot with Endnote meanwhile, but that implies I keep everything in the same library, which is not currently the case.

On July 8, 2008, 12:00 AM Jan said:

Does FF3 supports Zotero plugin? I really appreciate the list you got. Actually I really need to organize my PDFs too.

On July 8, 2008, 9:42 AM jreiswig said:

Yep, Zotero 1.0.6 works with Firefox 3. See

On November 24, 2008, 1:40 PM googleluvr said:

Google Desktop Search or Windows Desktop Search will find and tag PDFs on local disks, and can then tag them.

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