Kutti over at Jungfreudlich asked the question:
Thus I thought I would simply ask you! How do you organize your PDFs?
Here’s my setup at home (MacOSX):
- All papers that are worth keeping are entered into BibDesk, the best Bibtex editor out there.
- After each record in the BibDesk database is done I drag the paper’s PDF onto the still open window, at which point BibDesk renames and moves the PDF.
- There is no step 3.
This is the setup at work (Windows 2000):
- All papers that are worth keeping are entered into Jabref, a java based reference/bibtex manager. (Good to know: you can install it w/o having admin privileges.) Each project gets its own folder on a network volume.
- After each record in the BibDesk database is done I rename the paper using its “citekey” (=FirstAuthorLastName and Year).
- This PDF then gets filed into the corresponding folder.
- JabRef then can link to that paper.
Sorry, no screenshots available.
Further Tools for the job, only OSX:
- DevonThink Pro lets you search all PDFs in your reference folder, makes suggestions for similar content and much much more.
- KIT, also a snippet manager for OSX, which also helps organizing stuff.
- Papers, by former winners of Apple’s Student Design Awards. Pulls info from PubMed and organizes papers. If the above is too much hassle, THIS might be it! The authors are bio-scientists themselves…
- PDF-viewers that are better than Preview.app
- Check out the google group “The efficient Academic”
Feel free to ask any questions in the comments!
update 07-06-09: some more posts elsewhere: Labcoats, Miningdrugs
Just found this link for further mac tools:
MacScience: Reference management tools
Thx kayesdee for this great post! I have been looking at several of the links you posted and I found that Papers seems to be a great piece of software. The thing is that it only supports Pubmed but as chemists, we usually use Scifinder and download the papers directly from the source (e.g. webpage of JACS, Tetrahedron etc.) so this might be the sticking point.
About Bibdesk: you know that I used Bibdesk during my Bachelor´s Thesis but I didn´t like the fact that I had to fill in all the information about the paper (author, title etc.) by myself. I am still looking for an application, that automatically names the file after dropping it into the application.
Well… you have to switch your specialization then
BibDesk has some import features that are ‘a bit’ useful, but in the end you always have to do some work yourself. Since so many publishers out there just produce crappy PDFs (they consider the PDF as just a copy of the papoer version - i.e. no extra markup) you are left looking for extra help. As long as Scifinder is about the only way to access chemistry related databases you are also out of luck, as this app is just a rudimentary version of what it could be on the mac. (Its UI might not stand out as that bad on windows…). Feature-wise there is nothing that I know of that can do what you want.
Maybe Endnote (terrible and expensive). JabRef can import some of the exported citations from some publisher’s webpages and from scifinder, but still you have to look up the reference and import by hand. In that time you can also just enter the data yourself. In the meantime you learn the names of the folks out there
What could be possible is a script that looks up bibliographical data on the web, possibly via google scholar. It could be written in ruby or python… but someone has to do it
Again: this is what we have got on the mac so far. It is not perfect, but definitely workable. It takes about 30 seconds per paper to enter the metadata. Is that not worth it?
I like CiteULike for organizing my references. Then I just redownload the PDF whenever I want to read the paper. This may be a problem if someday I no longer have institutional access to journals, but at that point, I probably won’t want to read the papers anymore anyway1
CiteULike is great, too! Especially since you can import and export to bibtex! I believe the bookmarklet assists you in filling in the meta-data, but does it work with all journals? Maybe there are some problems with SciFinder-setups that don’t work via the publisher’s web pages, but rather directly link to the pdfs.?!
@kayesdee: Would you kindly change my name from “Kutto” to KUTTI in your post? I don´t want this typing error to spread (see entry in Mining Drug Space). Aarrghh!
Kutti: done. Sorry for the confusion. Long live the typo!
Check out http://sararah.livejournal.com/294817.html for some more takes on this, especially some notes about the mac software “papers”.
Hi,
The link for MacScience seems broken: here is the address:
http://www.macscience.net
Cheers,
S. Gadbois
MacScience.net