How To Upload Pdfs To Zotero

Photograph by Jake Lorefice on Unsplash

The Best Reference Manager Setup

(Zotero + ZotFile + Cloud Storage)

This article was originally published past Stephen Chignell  on Research Gate.

Introduction

This tutorial is the result of a couple of years of trying different software packages and reference manager setups.  After some trial and error, I've settled on a arrangement that is smooth, efficient, and complimentary.  The key is to use Zotero in conjunction with a cloud-based storage service. With this setup you volition be able to:

• Download, rename, and organize academic papers, news articles, web sites, and other reference fabric with one click.
• Have virtually unlimited storage for your PDFs with automatic back upward.
• Excerpt highlighted text and annotations from PDFs and associate them with references
• Search and insert references within a Word document and automatically insert a reference list in the required formatting mode of virtually any periodical.
• Create multiple libraries that you lot can share with collaborators and/or the public

Why Zotero?

• Gratis and open source
• Powerful and flexible
• Agile user customs

Function 0: Switching to Zotero

Many people may exist in a situation where they have already invested a lot of fourth dimension and money into a proprietary reference manager such as EndNote or Mendeley.  I used Mendeley for a couple of years before information technology was bought past Elsevier, who have since moved toward commercializing the software.

Equally far as I know, there are iii options for migrating your existing reference library over to Zotero:

1. Exporting your references from EndNote or Mendeley into Zotero is very easy. There are instructions for exporting from EndNote (hither and here) and Mendeley (hither and hither).
2. Exporting your references and PDFs might be a trivial more work, simply shouldn't be too difficult.
3. Exporting your references, PDFs, subfolders, and annotations is a flake more challenging, but is definitely possible. I retrieve Menotexport is probably the best way to exercise this from Mendeley, but there are other options out there too.
   • Note that as of June xvi, 2018, the Beta version of Zotero includes the power to import directly from Mendeley. However, Mendeley Desktop ane.19 has moved toward encrypting their database, so if you have already updated, you lot will have to follow the workaround in the to a higher place link to revert to an older version.
4. When doing a large import, Zotero may try to automatically find the associated metadata for each paper via Google Scholar. Nonetheless, after a couple hundred of requests, Google will suspect you are a bot and automatically put upwardly a CAPTCHA, which may boring or stop the import process. To avoid this, only disable your internet connexion during the bulk import; y'all can always go back and tell Zotero to look up citation information for specific files later.

While I'm pretty confident in this setup, I recommend going through the rest of this tutorial and trying out Zotero earlier doing any migrations, just to brand sure you similar it.

Office 1: Install Zotero Standalone and the Zotero Connector

1. Download and install Zotero Standalone AND the Zotero Connector
   
2. Configure Zotero Connector within your browser
   • Once installed go to Options à Config Editor
   • (Optional) modify the "Value" for automatic snapshots to "false" (double click)
     • If you leave it to "true" yous will get a copy of the spider web folio in your Zotero library. Some people like this feature, but I adopt to only attach PDFs.
       

PART 2: Install a cloud storage service

1. Cull your service
   • This could exist Google Drive or Dropbox that you already accept an account with.
   • Nevertheless, I highly recommend MEGA because information technology'southward gratis, encrypted, and gives y'all 50GB of infinite (which is essentially unlimited every bit far equally PDFs go)
2. Download the relevant desktop sync app (e.g., MEGASync)
3. Create a new folder in the syncing folder. This is where your PDFs volition be stored, so yous might want to give it an appropriate name like "Zotero" or "Zotero_Library" (see below)
   

Role 3: Install and configure Zotfile

Zotfile is an fantabulous improver for Zotero that helps to manage your PDFs.  It can automatically rename, organize, and extract annotations.

1. Visit the Zotfile site and download the xpi file (save as…in a folder you lot can find)
   
2. In Zotero Standalone, go to Tools –> Add together-ons
3. Click the gear icon and click "Install improver from file"
   
4. Navigate to and select the .xpi file for ZotFile that you lot downloaded
5. ZotFile should be installed, but y'all may need to restart Zotero

Setting up PDF syncing

Once Zotfile is installed, go into Zotero Standalone, select "Tools" from the top carte du jour bar, and click ZotFile preferences (you may need to restart Zotero beginning).

1. Go to the General Settings tab (meet below)
2. Gear up Source Folder for Attaching New Files to the desired binder
   • When you add a reference to Zotero, Zotfile will await to this folder for new PDFs to associate it with
   • Your "Downloads" folder is a adept option (this is what I apply)
   • Some people might prefer to use a separate folder as holding tank (e.one thousand. a folder on the desktop chosen "Papers for Zotero")
3. Fix Location of Files to "Custom Location" and point it to the folder you created in your cloud syncing app in Part two.
   

If you leave Use subfolder defined past unchecked, you will get a unmarried folder on the sync bulldoze with all of your PDFs in it.

Alternatively, you tin check this box to instruct ZotFile to organize your PDFs into subfolders by author name, twelvemonth, journal name, etc. (see the ZotFile website for more than info).

Personally, I find information technology more useful to leave it unchecked so all of my PDFs are put in ane big folder on the sync bulldoze (beneath).

I then make subfolders inside Zotero Standalone, since this is where I'll spend virtually of my fourth dimension navigating.

Gear up renaming rules

I strongly recommend instructing ZotFile to automatically rename your PDFs.  There are many options for this, simply here are the settings I use as an case:

Stopping automatic syncing to Zotero Cloud

When you make a Zotero account on Zotero.org and get-go to sync your Zotero Standalone library with the Zotero cloud, information technology volition default to uploading your PDFs along with your references.

However, we want to shop the PDFs in "My Library" to a separate cloud service using ZotFile, then we need to alter some settings earlier starting to sync:

1. Open the Zotero Preferences
2. Navigate to the Sync tab
3. Under File Syncing, uncheck "Sync attachment files in My Library using Zotero"
   

This is the primary setting that you demand to change in gild to have your references sync to the Zotero cloud, while your PDF attachments sync to your personal deject service.

As yous tin see from the screenshot, at that place are a number of other sync options that yous tin can suit.  To acquire more than about syncing with Zotero, I suggest reading the documentation (here).

Office 4: Install other add together-ons to Zotero Standalone

I highly recommend installing a Zotero Give-and-take Processor plugin (either for MS Discussion or Libre Office).

The post-obit plugins are non required for the overarching setup to piece of work merely they will brand your life easier and improve the overall feel.  For any of these, merely visit the plugins page and follow the steps to download and install the respective .xpi files like y'all did for ZotFile.

• Zotero Storage Scanner
• Google Scholar Citations for Zotero
• Zutilo
• FireTray
• Zotero QuickLook
  • This should work automatically with Mac
  • On Windows, you volition have to install QuickLook beforehand

There are many other plugins that I have however to try, including ones that enable integration with Google Docs and LaTeX.

I likewise highly recommend Unpaywall. This is not a Zotero plugin, only is added to your browser and will automatically search for open access PDFs on every periodical web page y'all visit.  If it finds an open-access PDF, Zotero volition usually grab it when you click the button.

Office 5: Using Zotero

You at present have everything you need to start managing your references with Zotero.  Zotero has many built-in features and there are many resources online for learning about these.  I'm therefore going to focus on some of the particularities of this specific setup.  Allow's start with an example.

Suppose yous come up across a paper that you would similar to download.  Let's utilize this PLOS Ane paper on antimicrobial resistance in foxes as an example.

The first step is to open the Zotero Standalone application.  One time Zotero is open, we tin can go back to the browser and notice that the icon for the Zotero Connector (ordinarily in the top-correct corner of the browser window) has changed to wait like a manuscript (encounter below).

This indicates that Zotero recognizes that there is a reference on the web page and that it is a journal article.

If nosotros were to click this push, Zotero would go to piece of work grabbing the reference information from the page and looking for an open-access PDF to download.  It would then announced in our library.

Nonetheless, I want to exist more organized and direct this reference to a subfolder (or "Collection"), non just my general library.  So before I click the push, I'm going to go back to Zotero Standalone and click the   button to create a new Drove.  I'll name it "Foxes".

Now go back to the browser and click the Zotero button. Lookout man and wait in wonder as the Zotero Connector grabs the reference and the PDF, and saves it to the "Foxes" drove in Zotero Standalone.

If you switch back to Zotero Standalone you should see the reference (red arrow) and the link to the attached PDF (blue pointer).  The column on the right shows the detailed metadata.

Meanwhile, in the background, ZotFile has automatically taken the PDF, renamed it, and moved it into your sync folder:

References vs. Attachments

This is an important moment to note that Zotero makes a distinction between the reference (or parent item) and the file(southward) associated with it.  If you lot wanted to, you lot could take a whole Zotero Library composed of references, with no PDFs at all.  Y'all can also have PDFs in Zotero that take no associated reference.

Continuing with our example, say you find this book on foxes and download the reference with the Zotero Connector.

Every bit you can encounter below, Zotero has the Volume reference, only no attachment. Our PLOS Ane paper, withal, has a blue dot, showing it has an attachment.

Double-clicking on a reference volition open up the associated file in default PDF viewer (I highly recommend PDF X-Modify Editor for Windows users).

I similar to comment PDFs with highlights or comments.  For example, open the "Mo et al" paper and highlight the showtime sentence of the abstract:

Save the changes to the PDF, and now go back to Zotero.

Correct-click on the reference, and get to Manage Attachments –> Excerpt Annotations

You lot should at present see a note attached to the reference, and the extracted annotation in the right-hand column.

Clicking the blue link will accept you to the relevant page in the PDF.

Hitting the green arrow in the top correct corner to sync your references to your Zotero Cloud (y'all will have to brand an account kickoff).  Remember, this is just syncing the references, non the PDFs (these are being synced by your cloud service).

Function 6: Deleting

There are a number of different options for deleting, and they're a trivial tricky with this setup. Normally, to delete an entry, you only correct click and select "Motion Item to Trash".

However, because we are storing the PDFs outside of Zotero, moving items to the trash volition only delete the reference, not the PDF.  I recommend deleting the PDF get-go, so deleting the reference in Zotero.

1. To delete the PDF, correct-click on the link to the zipper and cull "Show File". This volition open up up your storage folder in a new Window where you tin can delete the PDF as you would any other file on your computer.
   
2. At present that the PDF is deleted, go to Zotero, right-click on the reference, and select "Move Item to Trash":
   

Function 7: Other tips

Yous at present accept the nuts of downloading and managing references in Zotero! There are many other corking functions bachelor in Zotero, and the all-time way to learn is to commencement exploring the program. The Zotero documentation and forum are also nifty places to commencement looking for tips and tricks. Here are a few functions/options that I find peculiarly useful:

Other ways to bring a reference into Zotero

1. Drag and drib a PDF into Zotero Standalone. Zotero volition attempt to detect the right metadata and create a reference for it.
2. Sometimes this doesn't work, and you lot can right-click and say Retreive metadata for PDF.
   
   
3. Possibly y'all take a DOI but no PDF. You lot can click the tool at the tiptop of the Zotero Standalone window, and paste a DOI or other type of identifier into it. If Zotero tin find a matching tape online, it will create a new reference in the library.
   

If you larn the relevant PDF at a later date:

1. Put it in the Downloads folder on your calculator (or whichever folder yous selected for Source Folder for Attaching New Files in the ZotFile settings in Office 3).
2. Go to Zotero Standalone and right-click on the reference
3. Select Add attachment from source binder
   
4. ZotFile will grab the PDF, rename it, move it to your sync folder, and acquaintance the reference with it in Zotero, just as if you had clicked the Zotero Connector push button in your browser.

Setting up RSS Feeds

If you sign up for table of contents alerts from your favorite journals, you might consider sending them direct to Zotero via an RSS feed.  Here is how to practice it.

Recursive folders

If yous're like me, you like it so that selecting a collection folder will testify all the references in that folder and all sub folders. This is not the default for Zotero, and tin exist easily changed by the post-obit steps:

1. Open Zotero Preferences
2. Go to the "Advanced" tab
3. Click Config Editor (it may give you a alarm, merely ignore it)
4. Search for "recursive" in the search bar
5. Change extensions.zotero.recursiveCollections so that Value = true (double click on the discussion "false")
   

Searches

There are many means of searching your Zotero library. It's worth reading through the search documentation to become a sense of what's possible.

Open URL

Consider setting upward an OpenURL  resolver to help place references with the "Lookup" push. This can exist very useful, peculiarly if your institution or system has a library that gives you access to journals. Here are instructions.

Deleting PubMed entries

Some journals, such equally Science automatically download a PubMed metadata attachment to the reference.  This can be annoying because it will seem similar the reference has a PDF attached, when in fact it'due south just the PubMed entry.

I suggest creating a saved search which will identify any references with a PubMed zipper. Once it'south set up, simply check the search once in a while, and delete the PubMed entries. Here are instructions.

Groups

Groups are incredibly useful when working with collaborators.  A couple of notes virtually groups:

• Each of your group libraries is distinct from each other and from your personal library
• You lot tin can easily drag references from one grouping to the other
• If you lot followed the setup in this tutorial, your library PDFs will exist stored and synced in your deject service. However, your grouping PDFs will exist synced on Zotero'due south cloud, which gives you 300 MB for free, and larger storage plans for an annual fee.

Happy Researching!

Stephen Chignell received an M.S. in Watershed Scientific discipline from Colorado State Academy in 2017. His primary's research focused on water issues in Ethiopia, where he analyzed links among urban growth, hydropower, and big-calibration land acquisitions, and conducted baseline mapping of the state's unique alpine wetlands. Recently, Stephen has contributed spatial assay and training to the Secondary Cities Initiative, and worked to reconstruct the history of Antarctic science with the McMurdo Dry Valleys Long-Term Ecological Research project. He will be starting a Ph.D. in the Institute for Resources, Environment and Sustainability at the University of British Columbia in 2018. You can observe more than about Stephen'southward work or contact him through his ResearchGate page. (Bio photo credit: Josh Darling)

Source: https://www.nrel.colostate.edu/set-up-best-reference-manager/

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