Thursday, February 16, 2012

One of these days, I'm gonna get myself organazized.


I have a lot of articles in pdf form. Probably close to a thousand of them. I've kinda got them organized in folders, but I'm increasingly finding it unwieldy, especially when I need to find an article. The searchability of pdfs tucked into folders is pretty limited. So I end up downloading the same articles multiple times. Such a terrible waste of pixels. I need an easier, better, more searchable way to archive this stuff, preferably one that lets me search keywords and content, without my having to actually do any work keywording and stuff. Something that would also make it easier to cite and reference would be fab. I used DevonThink when I worked on my diss years ago, but it required too much effort, and didn't work very well, so I got nowhere with it. Suggestions?

~zombie

p.s. I'm a Mac.
p.p.s. That's not my office. My office has no windows.

27 comments:

Anonymous said...

Yikes! I had a colleague once whose office looked like that. The campus fire marshall declared it a fire hazard and ordered him to clear it out -- or they would trash everything themselves. He ended up renting a Public Storage unit. You might be living on borrowed time!

Anonymous said...

This does most of what you want:

http://www.mekentosj.com/papers/

I don't know about the Windows version, but the Mac and iOS versions are really well done. If you're still a student, there's a big student discount available, too.

Anonymous said...

zotero

Anonymous said...

Sounds like you need mendeley. It's like itunes for pdfs, but without the horrible bloat.

It's free and available for linux, mac, and windows. It also has a pretty nice syncing system, like dropbox.

It has a plugin for word/openoffice/libreoffice to insert citations and generate bibliographies. It has continuous bibtex output, if you like latex.

The main downside is that its metadata extraction from pdfs is a bit weak - when I add a new pdf, I often have to manually tweak the title/journal title/etc.

Anonymous said...

I had the same problem! Here's what I did:

I developed a spreadsheet. Author, article title, general topic, and (in some cases) a one-sentence description. Then, I alphabetized all of my print-outs of articles (PDFs I named with author's last name, underscore, first few words of the article title). Every time I downloaded or printed a new article, I immediately added its information to the spreadsheet. If ever I wanted to look up an article (or figure out if I had it), I didn't have to go searching through files or folders -- I just had to look at the spreadsheet.

Anonymous said...

http://www.mendeley.com/

This is also a great PDF organizer.

Anonymous said...

A second vote for Papers. I've been using it for 4 years and it revolutionized my workflow.

Anonymous said...

I'll second Papers.app. It's very nice. (It also includes a slick citation-insertion/bibliography compiler/reference manager on the mac side. Except that you can't insert citations in footnotes! Aaaa!!1!)

Anonymous said...

Calibre works really well for ebooks, and is freeware: http://calibre-ebook.com/ You're probably familiar with it if you have a kindle or some such, but it's a pretty useful organisational tool even if you haven't.

You could probably make it work for pdf articles as well, if you spent some time tagging them with various bibliographic/content info. But I don't think you could get it to export bibliographic info.

Anonymous said...

I'd also throw my support behind Mendeley. It's great for sorting, searching and reading PDFs, decent for annotating them, and with decent BibTeX output support (except on @incollection vs @inbook, if you care).

I find their web interface kind of clunky (the search is terrible), so I just let Mendeley organize the PDF files, but then have that folder in my dropbox for remote access to all my papers (including via mobile with the Dropbox app - which can be helpful to check quotes or citations).

Anonymous said...

I use Mendeley and find that it works well.

Anonymous said...

I've used ReadCube, which is all right. But ultimately, I find that my own e-filing system is much simpler (I file things according to broad categories and specific problems). When that fails, I search via ReadCube.

This is not the advice you're looking for, but that office looks like it's been victimized by a hoarder. Take it from a fellow hoarder and assert control while you still can.

zombie said...

For the record, that is not my office. That is a RW representation of my digital files.

I should have mentioned I'm a Mac user.

Anonymous said...

I do my own file management. When I download a PDF, I always title it the same way: AuthorLastName YearPublished - PaperTitle. Those are sorted into general categories in a folder, but usually I'll just search on my computer. I've never had problems locating my articles that way. This wouldn't necessarily solve the problem of searching the text within the article, but if you're mostly looking for author or title, I find this to be a quick and easy solution.

Anonymous said...

You might try grep. Grep searches text inside documents, so if you have an idea of what you are looking for, you can just grep a bunch of files. It looks as if Macs have further search capabilities with Spotlight: see http://pages.uoregon.edu/noeckel/Searching.html

Anonymous said...

I use bookends for mac. It's a great bibliography program that allows you to attach PDF's to entries. It interfaces great with my preferred word processor, Mellel, and also work with Word, though I haven't tested that aspect very much.

Anonymous said...

I second Calibre, and you should also look into Evernote. Evernote is an app, and has a monthly charge for certain services, but it has powerful search capabilities: i.e. it can search .pdf's.

Anonymous said...

I use bookends on my mac (See here http://www.sonnysoftware.com/). It is a referencing tool but you can attach pdfs to each reference file. It labels the pdf files as you attach them with author and date and moves them to a single folder so even if you aren't running the program you can search for pdfs easily (e.g. the bookends attachment folder is in my dropbox so I always have searchable access to my pdfs on my phone or other folks' computers).

Anonymous said...

If you're still using LaTex, check out BibDesk. It's free. It's made to connect with LaTex but you can use it without LaTex, too.

Anonymous said...

The word from the developers is that the next big update of Sente will include the ability to search within pdfs--when that happens it will become a great option for the kind of thing you are looking for. I have no idea how long it will be before that update comes out, though.

Anonymous said...

JabRef is another BibTeX frontend; it's Java-based, so it should work cross-platform.

Anonymous said...

On a Mac, you just have to type a word or phrase or author or title in Spotlight. It's never been easier for me to find the pdfs I'm looking for.

That said, it looks like Mendeley is the the consensus of the thread. And it's free, so I'm downloading it to check it out.

Anonymous said...

definitely papers.app!

Anonymous said...

Zotero is the best. Makes it easy to import into the database directly from your browser. Given the excellent metadata extraction it has for most academic publishers, this means you rarely ever need to edit info fields.

Combine that with note storage, syncing, and full-text search. Free as in beer, free as in speech.

www.zotero.org

Anonymous said...

I strongly endorse Papers. It has a smooth interface, and supports automated metadata matching on batch pdf imports (ie drag a folder of pdfs onto the window and it will automatically try to identify their bibliographic information for you -- only works about 30-40% of the time for philosophy in my experience, but that's a big help for lots of pdfs.) It's most recent version has also added a nice and intuitive interface for highlighting and annotating pdfs within the application.

Anonymous said...

Mendeley ftw.

Andrew N. Carpenter said...

Mendeley is the best tool I've found.