Papers
For a while now, I’ve been using a great programme called Papers to organise PDFs of journal articles along with their associated bibliographic metadata. I use the terrific BibDesk for the output side of references (formatting references into citations and a reference list in manuscripts), but I didn’t find it so helpful for gathering, organising and reading articles. Papers, on the other hand, specialises in just those kinds of tasks.
You can do searches within Papers itself for articles, using a selection of the scientific databases like PubMed or Web of Science. You can also select a PDF you’ve downloaded outside of Papers, and try to ‘match’ the paper (using the same databases) to download the associated metadata. This is fantastic when it works, because it avoids a lot of tedious, error-prone typing of information.
My workflow is like this; I subscribe to various journal alerts for the areas I’m interested in, and get regular emails listing new articles, with links to the article online. If any of the articles look interesting, I visit the link and download the paper to my downloads folder. If I don’t have time to deal with the papers at that moment, they stay in my folder for a while. Then, when I’ve got time to process them, I drag them into Papers to import them. Papers renames the files in a consistent way, and also moves them to a particular folder to keep everything tidy. I used to have to then match the papers to download the metadata, a process which sometimes failed for particular journals, or for articles which were only recently published. However, in Papers 1.7, there’s a miraculous new feature which somehow automatically extracts the metadata from either the PDF or from the web site you downloaded it from on import. It’s tantamount to magic to me, but however it works, it’s a stunning feature and saves quite a bit of manual work.
Once the papers are imported, I flag them all, and can then view all my ‘To Read’ papers with a smart folder collecting together flagged items. As I read each one (the full screen PDF viewer within Papers is really nice), I tag it with appropriate keywords, then drag it into specific folders depending on whether it’s useful for a particular project I’m working on, or as a reference for a specific module I teach). I also drag it into a ‘For BibDesk’ folder, which I periodically export to BibTeX format and import into BibDesk, so that forms my canonical list of references.
You can also generate a papers:// URL for each reference, which when clicked, opens the reference in Papers. That’s useful when you’re writing notes on a paper in a text editor, and want a quick way of opening the original. It’s made the whole process of keeping up with the literature a lot easier.
1
Cor! That don't 'alf make me glad I'm fick!
I couldn't organise a booze-up in a brewery, don't understand people with brains like filing cabinets who understand the principles of making lists.
I have a simple working method, keep doing the bits I enjoy until I bump into a bit of the boring stuff, avoid it or get it out of the way as quickly as possible, then get back to the interesting bits - Unfortunately, the tedious times outweigh the good - still, pension time in 2 years, so it will be back to building loudspeakers, finishing the valve phono amp and record deck, moving nearer the coast, buying a small yacht and starting life...........
by Jonathan Briggs @ 29/02/2008 9:32 pm • Permalink •
2
I keep my database managed in bib-desk, and have to say that I rather like the experience, and I never found papers to be very useful, though I should take a look at it again.
Though I think my complaint about it was more that as a social scientist, all the article repositories that I wanted to use weren't hooked up or able to be connected properly. Alas.
You lucky biology folk.
by tycho garen @ 01/03/2008 3:26 am • Permalink •
3
Jonathan: The whole making lists thing is a bit compulsory in my line of work because you'd go mad or get shouted at by people for not doing things otherwise. Your retirement plans sound great to me
tycho garen: They've added quite a few more article repositories. There's Project Muse (not sure if that's any good to you), Google Scholar and Google Books and Web of Knowledge, which you can set in the prefs to search the Social Science Citation Index. Might be worth another look. I think it's improved a lot in the last couple of updates.
by bsag @ 01/03/2008 6:43 pm • Permalink •
4
Waaaaaaaaaaay off topic, but I think this is right up your street Bsag.
by Jonathan Briggs @ 02/03/2008 10:38 am • Permalink •
5
Oops! I can never tell whether these things are going to work, we'll do it the non techie way:
Waaaaaaaaaaay off topic, but I think this is right up your street Bsag:
http://www.willridgeimages.co.uk
by Jonathan Briggs @ 02/03/2008 10:41 am • Permalink •
6
But it's just for Mac! Dang!
by Full Grown Single @ 02/03/2008 3:49 pm • Permalink •
7
"..... until I bump into a bit of the boring stuff"
Jonathan, my system works a bit like your'n....
.... I'm a piler, not a filer. The problems arise when someone bumps into one of my piles :(
......................................................or moves them
by Jerry @ 03/03/2008 2:09 am • Permalink •
8
Too much information Jerry, too much information........
by Jonathan Briggs @ 03/03/2008 11:08 am • Permalink •
9
I think it's about time I got a Mac....
by Jerry @ 03/03/2008 11:21 am • Permalink •
10
Jonathan Briggs: Oooo, lovely photographs. Wish I could take wildlife shots like that - I'm very envious.
Full Grown Single and Jerry: It's always time to get a Mac
by bsag @ 05/03/2008 7:16 pm • Permalink •
11
Papers is the program I'm been looking for for ages. I've just spent the past three hours clearing out my downloaded papers folders and doing the tagging and renaming I always promised I'd get around to.
Cheers!
by Dave Mills @ 10/03/2008 12:18 pm • Permalink •
Page 1 of 1 pages