How to manage your PDF load

Climbing a Pile of Files

As a blogger but also as a psychiatrist I collect a lot of pdf files. Mostly articles retrieved via PubMed. We are still working on new guidelines for ECT which increases the amount of pdf’s on my Mac enormously.

Besides reading these pdf and evaluating them some of them are used in publications. So besides storing them in a way that I can can find them again I also use a reference program. Until now I used endnote as a program to insert references in a text. Endnote has a Mac version and I use it since version 3, it is now in version XI available.

I save all my pdf files in the same way, first year of publication followed by the first author and title of publication, e.g. Nobler MS, Teneback CC, Nahas Z, Bohning DE, Shastri A, Kozel FA, George MS. Structural and functional neuroimaging of electroconvulsive therapy and transcranial magnetic stimulation. Depress Anxiety. 2000;12(3):144-56, becomes: 2000-NoblerMS-Structural and functional neuroimaging of ECT and TMS.

Endnote also has the possibility to attach a pdf to a reference, an option that I don’t use very often. Until recent I used Yep to store my pdf files. When you start yep for the first time it scans your hard disk for pdf files. You can tag those files, you can make collections based on these tags and you can make smart collections so that every time you add a certain tag to a pdf it will appear in the smart collection. It doesn’t have a hierarchical structure and it places the pdf in maps with the year of addition instead of publication. When you have many pdf files it becomes cluttered, you need the “Loupe” to find the right pdf. When I changed from computer the whole of the yep library was disrupted, had to start tagging most of the pdf’s again.

In comes Sente and Papers. First Sente. The advantage of Sente is that you can drop a pdf file in it’s window and it will start searching PubMed and other online reference databases. Sente will automatically create and populate references when you import your existing PDF files. It will file and rename PDFs and other attachments based on your preferences. It also works the other way around. You can search e.g. PubMed and retrieve the pdf’s which automatically gets into your reference library.

The search function for PubMed is somewhat limited. Advanced searches are not possible from within Sente. You can safe your searches and keep up with new articles on the search subject. If Sente doesn’t recognize the pdf you can search by copying the title or authors and sente will search in the online databases and you can accept the right suggestions by Sente. Moreover, you can import your old endnote reference library and use sente as your reference manager. Sente works directly with Apple Pages ’08, Microsoft Word, Mellel, Nisus and others so that you can easily insert citations and bibliographies, in any format, into your documents.

To download most of the pdf files I have to retrieve them via our institution library. I haven’t figured it out yet how to accomplish this with Sente and having to go to the site of our institutional library.

Another disadvantage is the price: 129,95 US Dollars.

Papers is much cheaper, 42US dollars. You can import pdf files. Pushing the match button will hopefully retrieve the right data from pubmed. I found it to be less accurate than Sente.

This software works even better the other way around. Searching Pubmed and importing the pdf files was easy. Still have to figure out the retrieval with our institutional library. The advanced search facilities are also limited.

Importing my Endnote library of references was a breeze. Papers also remembers past searches and also has the option of a number of predefined search terms. You can also create groups of papers, and smart groups where any paper in your library will be included that meets certain criteria.

Papers doesn’t insert citations and bibliographies into your documents. But has some other nifty features, you can read your pdf in full screen mode, and you can easily print or e-mail the pdf from inside Papers.

And the last option is iPaper. iPaper is a little bit spartan. It only retrieves the information from pubmed when provided with the PubMed ID (PMID). You can search PubMed from within iPaper and download the pdf in iPaper, but that sums it up. It is freeware.

You can even use iTunes to simply collect your pdf files. You can search, describe, and rate PDFs just like you do the music files. Radiologists at at Renji Hospital and Shanghai Jiaotong University School of Medicine in Shanghai are using iTunes to save, sort, and search PDF files. It is simple, cheap (free) and easy but without features such as searching and retrieving information from PubMed. For a how to use iTunes for pdf files have a look at an article on about Organize your PDF library with iTunes

iPaper is to spartan and yet has to little features to fulfill my needs. Sente has all the possibilities I need although I have to test the citation and bibliography functions. Papers is cool but lacks the possibility of citation and bibliography making. So it all depends on what you really need. Sente and Papers both have a trial period so start with some testing as I did.

Was this helpful for anyone, did I miss some other solutions? What do you use to manage your pdf load?
Let me know in the comments.

Thanks to for some inspiration