Newbie Issues with PDF files?

Dave12042024
I have roughly 500 papers stored in PDF files. I want to catalogue them.
I was hoping Zotero would streamline this process?

1. Is there a way to edit the name of the file I have dropped into Zotero?
2. Is there a better way to search for words in the title?
3. Where are the PDFs I drop into Zotero stored?
4. Is there an easy way to get the title if Zotero can't find it in the data

Thanks
Dave
  • DonnaCoxBaker
    Hi, @Dave12042024. There are several factors that shape how to answer your question. First, you need to decide if you are going to embed the PDFs in Zotero or link out to them where they sit on your drive. If the second, you drop them into Zotero while holding your Ctrl and Shift keys--or the Mac equivalent.

    Before you drop your PDFs in, there are a couple of flags to turn on in your Settings (called Preferences in v. 6). In the General tab, select "Automatically retrieve metadata for PDFs...". If your PDFs have usable metadata, Zotero will create a parent citation info item and fill in the blanks it can.

    If you want to rename the files automatically as they're drawn in, choose "Automatically rename locally added files." You have several options about what the renamed file will be. Again, it has to have metadata to do this. If you also flag "Rename linked files," it will rename the file that sits on your hard drive, if you're linked to external files.

    If a PDF is dropped in and does not create its own parent citation info, you can do it manually by right-clicking on the PDF and choosing "Create Parent Item." If you don't have identifying numbers, like a DOI, you can do it manually.

    You can also manually rename a PDF by clicking on it in the catalog (center pane). You'll see its name appear in the right pane. Click in that, and it will prompt you for a new name and ask if you want to rename the associated file.

    Assuming you have dropped your PDFs into Zotero without linking out to them where they were, your PDFs are now in many different folders under this file path, unless you manually chose a different place in your settings:

    C:\Users\[your name]\Zotero\storage

    Searching for your PDFs will be best handled by creating the parent items for them. If you have already dropped them into Zotero without flagging Zotero to extract the metadata, you might want to delete a few and experiment with pulling them in with the flag selected to extract metadata. If that works better, delete all of the ones you dropped in (assuming they still exist on your hard drive), empty your trash, and give it another try on the whole batch. Some may not have good metadata, and there will be a bit of work to do to create the parent items.
  • Dave12042024
    Thanks for your quick and thorough reply. Thanks for clarifying where the files are stored. I dragged mine from my Dropbox

    I should have read the documentation more thoroughly before dropping 500+ papers into Zotero in various collections.
    My General Preferences are ALL set to on. I had naively assumed that the titles for papers would appear. Ideally, I would like the file names to be the same as the titles. Doing this manually will take me far too long. Perhaps there is another utility which is better for getting the titles from PDFs? Seems like a problem today's AI should be able to solve. Searching also seems weak unless one can use regular expressions.

    Do you know if there is a way to give something like Google Scholar a bulk request of PDFs and have it provide DOIs?

    Thanks
    Dave

  • DonnaCoxBaker
    If possible, Dave, I'd try removing them from Zotero and doing it over in one big batch, if you haven't done things to them beyond the import yet. I don't know what can be done with Google Scholar. Perhaps someone else has an idea on that.
  • Dave12042024
    I've spent a couple of days putting them into collections and dealing with duplicates. Is there an easy way to export what I have and reimport them so I don't lose the work I have done?

    Thanks
    Dave
  • DonnaCoxBaker
    Maybe import the second batch and leave the first where it is. Then perhaps you can merge your duplicates. It would be one by one, but really fast, I think. I've never tried to merge an orphaned PDF to a parented one, so try one first.
  • adamsmith
    edited January 7, 2024
    You can't merge top level attachments into existing items no. Google scholar has no ability to serve as a query interface and will also very quickly lock you out if you try to do anything automated. (Also no DOIs as far as I know).

    Could we take a stab back? What type of PDFs exactly are these? If they are contemporary(ish) journal articles, with original (rather than self-scanned) PDFs Zotero should successfully retrieve metadata for 80%+ --if it doesn't, something might be off. I have a hard time following the rest of this, but I think that should get us started.
  • Dave12042024
    Sorry wasn't clear... I have all the PDFs I want - dropped into Zotero, and organized into collections, duplicates removed. likely 60-70% had metadata. What I would like to do is export my library to a Folder /My1stZot. I can then easily rename the files more appropriately. THEN I would like a simple way to load all of these back into Zotero ideally keeping them in the same collections. Is a collection preserving export and import possible? Thanks
  • adamsmith
    That's not going to be reasonably possible, no.
    Collection preserving import export works using Zotero RDF, but re-import of files will break if you rename them.

    But if you have the right metadata (do you? still not sure) you can just change Zotero's rename preferences and bulk rename all files from within Zotero? What you suggest seems rather convoluted
  • Dave12042024
    Adam,

    1. Thanks for clarifying that import/export would be problematic.
    2. My clear preference is to efficiently rename files in Zotero. Appreciate it if you briefly explain how one goes about bulk renaming files within Zotero.
    3. Is there a bulk capability to update other properties such as authors, and links?

    Thanks,
    Dave
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