How to organize scientific article pdfs?

January 18, 2008 3:21 PM

Scientists: What's the best and simplest way to organize, annotate, and take notes from scientific journal articles on a PC? I'm starting a new project and ready for a new system that doesn't require four programs or being unable to find something when I can't remember the title or author. How do you organize your references, pdfs, and notes?

I used to print articles out, take notes in a physical notebook, and use EndNote for general bibliography and light searching uses. However, I found that I often couldn't find again what I wanted. Connecting required information with reference with notes with actual hard-or-digital copy of the article required multiple programs and notebooks, time, and frustration. Help me find something better?

What I want is a system that will allow me to:
1) use tags rather than folders to organize and search articles by subject matter.
2) allow easy searching/browsing by author, journal, date published, etc. (so, something that will easily extract and store the PubMed details of each item).
3) (ideally) allow me to search, annotate, take notes on, and read articles all in one place or with minimal fussing with multiple programs.

The Papers program for Macs looks awesome and just what I'm looking for, but I'm on a PC. Is there any similar program for PC users? Lacking that, how do you store your articles, keep notes on what you've read, and make it easy to find what you're looking for later?

posted by JustWandering to computers & internet (18 answers total)

Doesn't answer your software question, but for finding scientific papers, google scholar is your friend. Google also runs a patent search site which can be handy for some kinds of research.
posted by TeatimeGrommit at 3:24 PM on January 18, 2008

Zotero, the Firefox extension.
posted by Emperor SnooKloze at 3:39 PM on January 18, 2008 [6 favorites]

I'm good at finding the papers...it's just after that that my organization falls apart. I've tried Google Scholar, and I've found it to be useful when Pubmed fails. Its tendency to not always show the whole title irks me, though.
posted by JustWandering at 3:43 PM on January 18, 2008

It's in no way perfect, but I recently decided that the best method for me was to stick to a program- and platform-independent method of just renaming the files and storing all my searchable information in actual titles. I usually follow the format:

Lastname 2008 The entire title including any subtitles.pdf

but this occasionally gets augmented to:

Lastname et al (including Otherauthor) 2008 The entire title including any subtitles [keyword1 keyword2 keyword3].pdf

Then, I can use the normal operating-system searches for basic queries about names, title-words and dates. A more advanced search, like Google Desktop, could then be used to do more advanced searches.

I still don't have a good method for storing notes in an intelligible fashion... I would like to stick to textfiles, perhaps named in the same fashion, but I haven't figured out a way to store them so that I'll actually update them (a proprietary database wasn't working; a common spreadsheet might... but I haven't done that yet). Regarding the time associated with renaming: yes, it's a pain, but I renamed about 1500 files over my "holiday" in about 10 working hours
posted by zachxman at 3:46 PM on January 18, 2008

One word: Zotero. I used to use bibtex with my own filesystem based sytem for pdf storage and notes, and I and hate endnote for a whole stack of reasons. Zotero works ok with my previous system, and endnote is now completely irrellevant to me. Zotero is the future for bibliographic management for researchers without a doubt.
posted by singingfish at 3:52 PM on January 18, 2008

Endnote's usefulness has been lost on me for a while now. I too read a lot of papers and sometimes can only remember a phrase or so for searching. Thanks for asking this question and thanks to the people who have suggested Zotero - I'm excited to try it.
posted by wfrgms at 4:08 PM on January 18, 2008

I gave this answer in a previous thread with a similar question. It still works great and is fairly simple to implement.
posted by SBMike at 4:08 PM on January 18, 2008

If you have web space available somewhere and are willing/knowledgeable about setting it up, Aigaion could be good. I played with an old version a long time ago and liked it, and will be trying the new one to see if it's worth my moving in to it. (I'm a mess, but my subject area is obscure and small enough that usually with bookmarks and scattered download directories of papers I can manage, but I still feel ashamed of myself, heh.) In a similar vein, I was just playing with Nexus, but it's not so good at keeping all the different information and is more folder-oriented (though it does have tags). The good thing about it is that is has a clever solution to the typical problem of uploading biggish files (PHP restrictions on most web space will corrupt them if you go over the individual upload limit, which can be a royal pain... many old scanned papers are huge compared to the actual text content) without you having to tinker with configs in your web space provider. Or you can try running Aigaion in your local machine (I've never tried it but I suppose it should work if you have all the server software for a local host thingy).
posted by Iosephus at 4:12 PM on January 18, 2008

citeulike.org is a free online reference manager that supports tagging, has a bookmarklet that you can click when looking at a pubmed (or other online database) page to automatically add the references.

It is social, so that you can access other people's tags, join groups, and search for related articles. You can add notes to your references that can be public or private, and if you upload the pdf version of an article, you can access it from any computer (you must log in to access saved pdf files to avoid copyright issues). You can import BibTeX and export BibTeX or Endnote.

I've used it a bit, and have been happy with it.
posted by i love cheese at 4:20 PM on January 18, 2008

You can put URL's in Endnote, you can put notes in Endnote, you can put abstracts in Endnote, you can categories your articles in Endnote by using labels or other keywords. You can order by author, title, category, label and you can search on any field. If you save all your electronic articles to one place with a simple system say author_title.pdf, then a simple search in Endnote will make it easy to retrieve.
posted by b33j at 5:02 PM on January 18, 2008

Perhaps EverNote would work as a general bucket. I use BibDesk (Mac), so I don't know what would work best. You could try a file system approach though:

/project_name
  subject/
    authors.article_title.pdf

For search, Google Desktop might work. Foxit PDF reader allows for annotation.
posted by fleeba at 5:45 PM on January 18, 2008

Wow I just downloaded Zotero and it is impressive!! Thanks for the tip.
posted by peacheater at 5:57 PM on January 18, 2008

Another great program is IdeaMason. Very comprehensive, allows full referencing of academic articles, etc.
posted by worldshift at 12:27 AM on January 19, 2008

Nthing Zotero - it's wonderful.
posted by greycap at 1:12 AM on January 19, 2008

Same as peacheater and greycap; just downloaded Zotero and it's amazing. Why didn't I know about this before?!

I heart Mefites.
posted by Blacksun at 7:47 AM on January 19, 2008

Zotero
posted by chrisalbon at 9:42 AM on January 19, 2008

Personally I'm a big fan of JabRef. Features I like include:
- bibTeX-based file system, so it's trivially simple to include references when I actually write papers in LaTeX.
- Good indexing system for .pdf's. Once you create a citation, just point it to the pdf URL and it downloads it, renames it according to a scheme you setup (ie. AuthorYear.pdf), and stores it in a designated folder. From then on, one click and the .pdf pops up.
- Categories make it pretty easy to sort and find papers
- Each citation has a "notes" tab where you can type a review
- There is a network sharing feature, though I haven't used it

Anyway I'm tempted to try Zotero after seeing all the good press here, but JabRef has been serving me quite well.
posted by PercussivePaul at 3:18 PM on January 19, 2008

To search PDF (etc.) contents I use Copernic Desktop Search. It also previews your files without you having to open them. For PDFs Foxit, as previously mentioned, is pretty good, but I prefer PDF XChange Viewer. It uses tabs for different files (like Firefox) and allows you to mark up PDFs to your heart's content. Another great program for when you're cutting and pasting from PDFs into Word (etc.) and have to deal with word-wrapping-problems is the marvelous little program, UnWrap. Zotero too, of course. And to re-order open programs on the taskbar (to keep the flow going) try Taskbar Shuffle.
posted by rumbles at 11:10 PM on January 19, 2008