PDF annotation

gcompitello
I've recently lost all of the file links in Zotero, so I'm using this as an opportunity to reorganize my library.

I'm starting with PDFs on my hard drive (and SkyDrive and Dropbox) and re-importing into Zotero. The file path after importing is different the the path on my current drive(s.

For example, the path for this article:
C:\Users\User\SkyDrive\Endnote Refmanager and Papers\SciPapers by Category or with Supplement\refs\Journal club\01-16-06 BT

became:
C:\Users\User\AppData\Roaming\Mozilla\Firefox\Profiles\264u9wyd.default\zotero\storage\955DP69K

...which leads me to ask two questions:
1) Neither file has a name that means anything out of context. I've "Renamed from parent metadata" in Zotero (meaning the filenames aren't even the same anymore), and the file structure from my PC (skydrive) that told me where the paper came from (Endnote refs, Journal Club 2006, Presented by "BT") is gone from the Zotero ref (so I don't have that information, and can't even relate it back to the original file).

Also, the notes I made in the PDF (opened in Foxit from Zotero) are not with the original file (on Skydrive), but appended to one copy only, making it that much more difficult to search by MY notes.

So how do I keep separate files, with separate sets of information about a paper in sync with one another? Not all of the information is important, I'm juts tired of duplicating entries and spending sooo much time cleaning up / maintaining my scientific paper library - only to find that the information gets lost in the ether.

and (as if that wasn't enough)
2) Does this mean that I now have two copies of a PDF eating up space on my hard drive?

Any suggestion about how to keep all of my notes in a single copy of a PDF, but also use Zotero to manage the collection would be greatly appreciated. I miss just picking up a paper and writing on in with a pen and always having my notes with my copy of that paper.

Thanks
  • adamsmith
    You can use "Attach link to file" instead of dragging a file to Zotero - that leaves the file in its old location and doesn't create a duplicate copy (which yes, your current systems of doing this does).
  • aurimas
    Re annotations, I use Adobe reader which is sufficient for me and annotations stick to the file. Not sure why your Foxit annotations disappeared. I thought they embed annotations in pdfs also. Perhaps your annotated a different copy of the pdf that did not get synced.
  • adamsmith
    it sounds like s/he had two copies of the file, obviously annotating only one.

    My approach would have been to try to fix the file links in the first place - it seems pretty hard to me to break Zotero file links - but that wasn't the question.
  • gcompitello
    Thanks for all of your comments! I'll try Adobe again today (instead of Foxit).

    The links are gone because I was saving locally and my hard drive crashed. I was able to recover some of the files, but some had to be downloaded again or copied from a cloud source. When I rebuilt my file structure, I decided to clean house a bit and go for a simpler file structure (meaning the links weren't valid anymore).

    When I encounter a file that's missing a link in Zotero, I click "locate" and try and point Zotero at the file's new location. The trouble is, Zotero doesn't recognize that I've done this. Browsing to the file in Win7 and clicking open does nothing to update the link (i get the same message the next time I click).
  • adamsmith
    Zotero distinguishes between files stored in Zotero and files linked to Zotero. The latter are distinguished by they key-link icon. Locate only works for those.
    If you want to replace items stored in Zotero with links to files, you'll want to use "Attach link to file"
  • gcompitello
    It works! Thanks again for all your help.
  • emiliano.heyns
    Is it possible (by setting or by plugin) to have Zotero default to this when dropping attachments on an item? I sync my PDFs to my e-reader, so I'd like to keep my own organisation intact, but I would also prefer not to have to manually attach-link each file by hand.
  • adamsmith
    no.
    You can look at Zotfile, though, which is able to move&link items automatically.
    http://www.jlegewie.com/zotfile.html
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