Thursday, May 1, 2008

Zotero

I often extol the virtues of Zotero as the finest tool for tracking references and storing and sorting electronic copies of your papers in a searchable indexable tagable way all within Firefox. For sorting new papers the Zotero button in firefox just makes things too easy. But for your existing library of pdf and ps files its a bit more of a hassle.

However, if you're in need of a monumental act of procrastination (as I was today) the following procedure seemed to work pretty well:

If the pdf already has a bibliographic entry in Zotero then just drag the file onto the Zotero entry to associate it. You can then delete the original file as Zotero has made a copy. If not, then...
  1. Right Click in the Collections window and Create A Collection called Unsorted Files
  2. Drag and Drop all your articles into this collection
  3. Go make some coffee or something while Zotero copies the files to its indexing directory. Firefox may ask you if it should continue or cancel the script...just click to continue
  4. Open up the new Collection you created Double Click a PDF to view the pdf in your browser
  5. You can now enter the bibliographic information by hand
  6. Alternatively if your looking at an academic article (i know i usually am) then it probably has a doi. If your very lucky that doi is blue indicating it is clickable if it is click it. This almost always takes you to a webpage that Zotero knows how to read. If it does then just click on the Zotero button to the right of the url at the top. If it doesn't then google the doi or title and author and you will likely find a page that does have a Zotero button you can click
  7. This created a new entry that has the correct bibliographic information and placed it into the Unsorted Collection. Now just drag the pdf file you started with onto the new entry and see that it placed the pdf under new entry in the tree structure.
  8. Finally, drag the new Zotero entry to the appropriate collection and then right click to Remove the selected item from the Unsorted Files collection (do not delete from library)
Note this creates a new copy of the pdf file in the Zotero Directory so you can now delete the original file if you like. Anyway, this was eight steps, but once you get going it does go pretty quickly. If you have a better solution or know how to automate this please let me know.

7 comments:

Ladybug said...

is that seriously more efficient than just putting in the refs by hand and then attaching the pdf?

SuperFlunky said...

Anytime 10 clicks with the mouse can eliminate 10 cut and pastes i consider it more efficient. Besides once you get into the swing of things it goes quite fast. Next time I do a batch of imports i will time it and post the import rate.

Ladybug said...

surely 10 tab-and-types would be fastest???? But I hate moving my hands off the keyboard, so maybe that's just me. Added bonus: change of information wd make it less mind-numbing and easier to fall asleep later.

SuperFlunky said...

Now your just yanking my chain. There is no way that 10 tabs and types are faster than 10 clicks. Remember also that were not talking about typing everyday words, but names, numbers, doi's, url's, and entire abstracts! Zotero imports it all and gets is right!

Also, if you want to make it less mind-numbing, do what I do: flip on iTunes or skype a buddy or watch doctor who.

jd said...

thanks for posting this. i was planning on doing that for some time now, but with 600+ papers in my (non-zotero) collection, i never really felt like it. how many did you import at once and how long did it take you?

jd said...

moderation enabled? how paranoid! ;-)

moderate this, dr. claw! (know inspector gadget? that's at least how the blog picture looks like)

SuperFlunky said...

Realistically you can import and verify two pdf's a minute. But thankfully it's pretty mindless so you can also watch a movie while you do it. For example, my marathon importing session was associated with a marathon Dr. Who session.