Contents

  1. Overview
  2. Set-Up
  3. Saving Papers
  4. Folder Structure
  5. Creating and Navigating Tags
  6. Checking for Duplicates
  7. Quick Tips
  8. Caveats
  9. Annotated Bibligraphies

Overview

Zotero is a reference manager that allows the lab to have a shared collection of papers and makes it easy for users to add properly formatted in-text citations and bibliographies.

Set-Up

1. Create an account

Create an account at this link.

2. Get added to the NDC_Lab group library

Send a message to the lab manager with either your Zotero username or the email you used to create an account. They will send you an email invite to join the group library.

3. Install the application and Chrome extension

While you wait to be added to the group library, download both the Zotero application and Chrome extension at at this link.

Once the application is installed, it should automatically install a plugin for Word, at which point you will need to restart Word. If it doesn’t auto-install, see this documentation.

4. Sync your account

To sync your online account with your local copy of the application, open the local application and navigate to: Zotero > Preferences > Sync. Click “Link account” and log in using your Zotero username and password. Zotero should now automatically update the group library as others add papers to it. However, Zotero can be manually synced via the circular green arrow at the top right of the application window.

Saving Papers

Before you save a pdf to Zotero, either via the Chrome extension or by dragging a pdf in from another local folder, check the main NDC_Lab folder to see if the paper already exists in the lab’s library.

  1. If the paper does not exist in the group library, save it to your project’s Triage folder; immediately add your project tag (e.g. ‘rwe’). Confirm that Zotero saved a pdf (not a snapshot) and that the metadata (authors’ names, title, year published, etc.) is correct. If necessary, manually correct the metadata.
  2. If the paper does already exist in the group library, do not save it again. Instead, drag it from the main NDC_Lab folder to your project folder’s Triage subfolder to “add” it to your collection of papers for triage.

Folder Structure

NDC_Lab Group Library

The group library can be thought of as a collection of songs. Each subcollection (folder) within it acts like a ‘playlist’ of certain papers. Papers that are removed from subcollections (playlists) are not removed from the group library (all songs) or from other subcollections.

Note that a given collection (for example, “my-project-folder”) does do not actually “house” its subcollections (Triage, In-Process, Annotated). Every collection and subcollection is an entirely separate folder and the nesting is only visual. As a result, papers and tags found in a subcollection (e.g. Triage) are not searchable from the main collection (my-project-folder), and vice versa.

Main project folder

No papers are saved in this folder. It only contains a Standalone Note that lists the conceptual tags that are relevant for the project.

Triage

This folder is a staging area for papers that may be relevant for the literature review. A lab member confident in paper triage will determine if the paper is relevant to the project and worth annotating.

  • If a paper passes triage, it gets added to the In-Process folder and removed from Triage.
  • If a paper fails triage, it gets removed from collection (NOT trashed from library as a whole), and the project tag is removed.

In-Process

This folder is for papers that have been confirmed as relevant for the literature review and now need to be annotated (or are actively in the process of being annotated). Once they have been annotated, they are removed from the In-Process folder and added to the Annotated folder.

Annotated

This folder is for papers that have been read and annotated for a literature review. Relevant conceptual tags are added to the paper when it is added to the Annotated folder.

Creating and Navigating Tags

Papers can be assigned tags and these tags can then be used to filter the library by topic. A project might have tags that refer to theories, concepts, or methods. The tags should be developed by members of the project and listed in a Standalone Note to ensure that all project members are using the same tags. A project’s Standalone Note lives in the main project folder.

Certain tags might be utilized for multiple projects. In order to make sure tags stay standardized across the lab, there’s a Standalone Note in the main NDC_Lab folder; this note contains labwide tags and is called “NDCLab Conceptual Tags”. When creating a project-specific Standalone Note with tags, copy over the labwide one and add a project-specific section to the top.

Papers in a subcollection or in the main NDC_Lab group library can be filtered by clicking tags on and off in the lower left-hand corner of the Zotero app. Clicking multiple tags will narrow your search further. Clicking on an already selected tag will remove it as a search parameter.

Checking for Duplicates

If you have added several new papers to the lab’s Zotero account, you should check to be certain that you didn’t accidentally create any duplicates.

  1. Click “Duplicate Items” at the bottom of the Group Library.
  2. Select any duplicates. The window pane on the right shows you the data for each item.
  3. Highlight the most complete item, then click Merge. This will merge the two records.
  4. Navigate to that record in the main collection and make sure it only has one PDF.

Quick Tips

  1. For an overview of all of Zotero’s features, click here.
  2. The Zotero app must be open and running on your computer for the Chrome extension to work.
  3. Once you save a pdf to a folder, it should automatically retrieve the metadata from the pdf so it’s accessible for citation purposes and so it can be sorted by the author, date published, title, abstract, etc in the Zotero app. If it doesn’t load it automatically, right click on a pdf in the app and click Retrieve Metadata. You may have to manually type in the info or correct the info it generates.
  4. Triage folders should include the project name in the folder name. When using the Chrome extension, this makes it easy for lab members to be sure they are saving a paper to the correct folder. Project names are not added to the In-Process and Annotated folders to reduce visual noise within the library.
  5. After selecting a paper within the app, you can highlight all collections that contain this paper by holding down the “Option” key on Mac OS X, the “Control” key on Windows, or the “Alt” key on Linux.”

Caveats

Avoid creating any modifications—like notes or highlights—to an article or journal under the Group Library entitled NDC_Lab folder on Zotero. Any modifications should be done so only after one has created an individual copy of the paper so that the changes aren’t reflected onto the lab’s archives.

To make an individual copy of a paper refer to the following steps:

  1. Locate the file for the article of interest under “NDC_Lab.”
  2. Drag the original file of the article onto “My Library.”
  3. Apply any modifications to the the article under this new file in “My Library.” (Tip for Mac users: Before adding notes or highlights to your own copy using Preview, go to File>Export as PDF, then swap out the Zotero file in “My Library” for this new export. This helps ensure stability in the modifications, which otherwise have a tendency to randomly disappear!)

Annotated Bibliographies

Each project should have a Google Sheet in its project folder for the annotated bibliography. When you begin reading and annotating a paper that is in a project’s In Process folder, add the citation to a new line and include your initials in the leftmost cell. To capture a citation, right-click the item in Zotero and select “Create Bibliography From Item.” The default is typically APA, with an output mode of “Bibliography” and an output method of “Copy to Clipboard.”

In deciding which papers to annotate, it is typically best to prioritize those that haven’t yet been added to the shared annotated bibliography. However, there is no harm in multiple team members annotating the same paper, as different readers will extract different pieces of information.