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How to organize scientific article pdfs?

  • 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 http://mekentosj.com/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?

  • Answer:

    http://www.zotero.org/, the http://www.getfirefox.com/ extension.

JustWandering at Ask.Metafilter.Com Visit the source

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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.

b33j

To search PDF (etc.) contents I use http://www.copernic.com/. It also previews your files without you having to open them. For PDFs Foxit, as previously mentioned, is pretty good, but I prefer http://www.docu-track.com/home/prod_user/pdfx_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, http://windowsutilities.com/unwrap.html. Zotero too, of course. And to re-order open programs on the taskbar (to keep the flow going) try http://lifehacker.com/software/windows/download-of-the-day-taskbar-shuffle-173143.php.

rumbles

Personally I'm a big fan of http://jabref.sourceforge.net/. 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.

PercussivePaul

Zotero

chrisalbon

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

Blacksun

Nthing Zotero - it's wonderful.

greycap

Another great program is http://www.ideamason.com/. Very comprehensive, allows full referencing of academic articles, etc.

worldshift

Wow I just downloaded Zotero and it is impressive!! Thanks for the tip.

peacheater

Perhaps http://www.evernote.com/ 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.pdfFor search, Google Desktop might work. http://www.foxitsoftware.com/pdf/rd_intro.php allows for annotation.

fleeba

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