Zotero deleting items

I have noticed that some of my collections have become quite sparce. I haven't looked at the items in a couple of months, but now that I return to the collection there are only a couple of items in it. I'm not sure what's going on here. I did not delete any items from the collection, and yet they are gone from the entire library. Same thing happens sometimes when I go back to check references for a manuscript that I wrote a couple of months ago. I find some references have been deleted from the entire library. I sometimes will merge duplicates, but that shouldn't remove them from the whole library or any folder. I checked the trash but wasn't able to find any of the items there. I have enough storage on the zotero website and automatic syncing. Has anyone had this problem?
  • Have any of those items been cited in a document? That might give us a way to trace what they were and what might have happened.

    Generally speaking, of course, Zotero doesn't just delete items. It can't. So something else is going on.
  • edited March 1, 2016
    Yes, I can provide you the citations if you'd like. I have had to re-add these citations to my zotero or else the citations would be off in my article. There are some that are still missing.
  • So what we'd need is a citation of an item that's no longer in your database, but still in Word and that you haven't re-added and re-cited.

    We'd then need you to hit alt+F9 in Word (alt+FN+F9 on Mac), which will display field codes (lots of code-looking stuff) for all citations. Just copy the entire field code for the item in question here.
  • ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"d5tdUs3a","properties":{"formattedCitation":"{\\rtf \\super 35\\nosupersub{}}","plainCitation":"35"},"citationItems":[{"id":587,"uris":["http://zotero.org/users/2517503/items/PVEPFSEA"],"uri":["http://zotero.org/users/2517503/items/PVEPFSEA"],"itemData":{"id":587,"type":"article-journal","title":"Progress toward the prevention and treatment of atrial fibrillation: A summary of the Heart Rhythm Society Research Forum on the Treatment and Prevention of Atrial Fibrillation, Washington, DC, December 9-10, 2013","container-title":"Heart Rhythm","page":"e5-e29","volume":"12","issue":"1","source":"NLM","archive_location":"25460864","DOI":"10.1016/j.hrthm.2014.11.011","ISSN":"1547-5271","shortTitle":"Progress toward the prevention and treatment of atrial fibrillation: A summary of the Heart Rhythm Society Research Forum on the Treatment and Prevention of Atrial Fibrillation, Washington, DC, December 9-10, 2013","journalAbbreviation":"Heart rhythm : the official journal of the Heart Rhythm Society","language":"eng","author":[{"family":"Wagoner","given":"D. R.","non-dropping-particle":"Van"},{"family":"Piccini","given":"J. P."},{"family":"Albert","given":"C. M."},{"family":"Anderson","given":"M. E."},{"family":"Benjamin","given":"E. J."},{"family":"Brundel","given":"B."},{"family":"Califf","given":"R. M."},{"family":"Calkins","given":"H."},{"family":"Chen","given":"P. S."},{"family":"Chiamvimonvat","given":"N."},{"family":"Darbar","given":"D."},{"family":"Eckhardt","given":"L. L."},{"family":"Ellinor","given":"P. T."},{"family":"Exner","given":"D. V."},{"family":"Fogel","given":"R. I."},{"family":"Gillis","given":"A. M."},{"family":"Healey","given":"J."},{"family":"Hohnloser","given":"S. H."},{"family":"Kamel","given":"H."},{"family":"Lathrop","given":"D. A."},{"family":"Lip","given":"G. Y."},{"family":"Mehra","given":"R."},{"family":"Narayan","given":"S. M."},{"family":"Olgin","given":"J."},{"family":"Packer","given":"D."},{"family":"Peters","given":"N. S."},{"family":"Roden","given":"D. M."},{"family":"Ross","given":"H. M."},{"family":"Sheldon","given":"R."},{"family":"Wehrens","given":"X. H."}],"issued":{"date-parts":[["2015",1]]}}}],"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"
  • @Dan -- any history of http://zotero.org/users/2517503/items/PVEPFSEA on the server?
  • edited March 2, 2016
    Yes, the item was deleted via sync on October 25th, along with 2000 other items.
  • @doctuppy -- unfortunately that's the best we'll be able to give you. With near certainty those items were actually moved to the trash in Zotero either by you or by someone syncing with your account on or shortly before that date, but we can't, of course, know the circumstances of that.
  • That sucks; let's work on a plan for next time. How can I prevent these kind of losses in the future? turn off automatic syncing? use one computer?

    I really need to keep my files intact in order to be an effective researcher! It's really frustrating chasing down articles that I should already have in my library. I was using Zotero on two computer and wonder if that's the problem. Is this possible? Would it be possible to set up the ability to turn syncing on/off on a particular machine?
  • These items very specifically moved to the trash. If you didn't do that, it's possible you kept your sync information on a shared computer and someone else did. This type of thing doesn't just happen during a regular sync, so the problem isn't that you were using two computers. You can turn sync on and off on any computer you use (just disable automatic sync in the preferences), but I'm not sure how much good that would do, since presumably you need syncing to work between your two computers. And not syncing, of course, also removes a layer of backup, e.g. if your harddisk crashes.

    The best protection is to have longterm, incremental backups. You want a setup along the lines of Mac's time machine: Keep daily backups for a months, monthly backup for a year, and yearly backups forever (or something along those lines). That should extend to all your important files and include Zotero. Any decent backup software can do this automatically and in the background.
  • edited March 3, 2016
    Just to be very clear, Zotero didn't do this — you or someone with access one of your computers did this, by explicitly deleting items. It doesn't look like these were even deleted as part of a merge (or at least the one above wasn't), but rather by actually deleting items manually. Perhaps you deleted a collection you no longer needed and accidentally chose the option to delete the items as well?

    If you're using multiple computers, we strongly discourage turning off automatic syncing. The only real answer here is to make sure that you don't delete items you want to keep and that if you're using Zotero on a public/shared computer you don't leave your sync credentials in the preferences. [Edit: Yes, and to use an automated backup system, as adamsmith says, to be able to recover from accidental mistakes like this.]
  • Is there a way to integrate my past backups with the new articles I may have added before I knew all of these files were deleted (I want to basically merge the backup and my current collection)? Is there any way for me to tell when a giant part of my library is deleted (to track down the day)?
  • as per Dan above, this would have happened around October 25 (2015 I assume). I don't think you'd be able to tell yourself, no.

    Merging the data isn't entirely trivial, since the delete log is saved and I can't think of a way to do so that wouldn't break links to Word documents for either the old or the new items.

    What I'd suggest doing is to export all items added to your library after the delete occurred. Then restore from a pre-delete back-up following these instructions:
    https://www.zotero.org/support/zotero_data#restoring_your_zotero_library_from_a_backup_and_overwriting_synced_changes

    Then re-import the exported items. They will no longer connect to the corresponding citations in Word, though.

    @Dan -- I'm not overlooking an option here, am I?
  • Is there an way I can program to find all the items which were imported after October 25? It's too bad that this will break links no matter how I do it (please, please tell me if I'm interpreting your post wrong). Any way this can be changed in the future so that merging is possible?
  • You can either sort by date added in the center pane (click on the little table icon to add the column if you don't see it) or you can do an advanced search for date added --> after and save it as a saved search.

    You only use the link between Word document and Zotero items. They'll still cite OK, they just won't be affected by any edits you make in Zotero, so this might not be so horrible.
  • If I change the paper so that some of the references are re-arranged or in a different order, will the citations update properly?
  • yes. All relevant information is in the document (as you can see in the thing you posted above). Only thing you need to be careful with is inserting new citations. Always make sure you insert them form under "Cited" rather than "My Library" (you'll see those as headings when using the red quick format window and searching for an item)
  • How do I differentiate between "cited" and "My Library" if I use the classic add citation dialog?
  • You can't get the cited ones with classic. You'll need to use quick format.
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