# Creating Symbolic Links for Zotero & Obsidian # A Step‐by‐Step Guide to an Integrated Zotero, Zotmoov, Google Drive, and Obsidian Workflow Research today can be complex given the number of applications around to "help" you. Keeping your PDFs, citations, and notes organised across devices is essential in providing access, irrespective of location or device. Whether it be phone or laptop when the work has been done at home on a desktop, the availability of information is important in any environment. This guide explains how to use Zotero as your reference manager, and then leverage the Zotmoov plugin to automatically move downloaded PDFs to a cloud‐based Google Drive folder. You could use Microsoft OneDrive or even Dropbox, but we will focus on integration with Google Drive for the purpose of this articele. Once in Google Drive, the PDFs can be integrated with Obsidian using a symbolic link. Follow these steps to create a seamless and accessible academic workflow to not only collect your articles, but also make them all available in Obsidian. ## Overview and Benefits First of all, let us summarise the benefits of implementing this workflow. - **Centralized Reference Management:** Use Zotero to collect and organise references. - **Automated PDF Organization:** With Zotmoov, automatically move new PDF attachments from Zotero’s default storage to a designated Google Drive folder. - **Pre-defined Renaming**: You can set the naming conventions within Zotmoov so the PDFs are renamed, i.e. Brown-2024 - **Cloud Accessibility:** Storing your PDFs on Google Drive ensures you can access your materials from any device. - **Secure Storage:** By storing your PDFs in the cloud, you are protecting your data from any losses. - **Save on Storage**: Storing your PDFs in the cloud will save you using up Zotero storage space. - **Integrated Note-taking:** In Obsidian, you can use a custom template that imports an article’s metadata (title, authors, year, etc.) into YAML front matter, making it easy to link notes with original sources. This is achieved using the Zotero Integration plugin. - **Future-Proofing:** The setup is ideal for researchers wanting a free, modular, and cross-platform solution. ## What you will need #### Zotero v7 You will need Zotero 7 and its browser connector so you can capture references easily. The plugins we will be using in Zotero are not compatible with earlier versions. If you already have plugins installed in Zotero 6, you will need to upgrade them. #### Zotmoov Plugin for Zotero Zotmoov automatically moves (or copies) new PDF attachments from the default Zotero storage folder to another location. #### Google Drive for Desktop Install the Google Drive desktop application to sync a designated cloud folder on your computer. #### Obsidian Your chosen markdown note‐taking app where you’ll store literature notes and integrate metadata via YAML. #### Zotero Integration Plugin Install this plugin in Zotero to move PDF articles into Obsidian for annotation. #### A Pre-made Obsidian Template A YAML template that imports head data (such as title, authors, year, and links) for each article. This template will be specified in the Zotero Integration plugin. ## Step 1: Set Up Zotero 1. **Install Zotero and the Browser Connector:** - Download Zotero from [zotero.org](https://www.zotero.org/) and install the desktop application if not already installed. - If installed, ensure you are using the latest version (Zotero 7) - Install the Zotero Connector in your preferred browser so you can add references with one click. 2. **Configure Basic Preferences:** - Open Zotero and create your personal library. - (Optional but recommended) Organise your references into collections (folders) as needed. --- ## Step 2: Prepare Google Drive for Cloud Storage 1. **Install Google Drive for Desktop:** - This app is essential for syncing your local drive with Google - Download the app from [Google’s Drive page](https://www.google.com/drive/download/). - Sign in with your Google account. 2. **Create a Designated Folder:** - In your Google Drive folder (on your computer), create a new folder (for example, “Zotero_PDFs” or “Zotero_Library”). This folder will store all your PDFs so you can access them from any device. --- ## Step 3: Install and Configure Zotmoov in Zotero 1. **Download Zotmoov:** - Visit the [Zotmoov GitHub releases page](https://github.com/wileyyugioh/zotmoov/releases) and download the latest .xpi file (e.g., `zotmoov-1.1.13-fx.xpi`). 2. **Install the Plugin:** - Open Zotero. - Go to **Tools → Plugins**. - Click the gear icon (usually in the top right) and choose **“Install Plugin From File…”**. - Select the downloaded Zotmoov .xpi file and follow the prompts. - Restart Zotero if required. 3. **Configure Zotmoov Settings:** - In Zotero, go to **Edit → Settings** (or Zotero → Preferences on macOS) and select the **ZotMoov** tab. - **Directory to Move Files To:** Set this to the full path of the Google Drive folder you created (for example, `G:\My Drive\Zotero_PDFs` on Windows or the corresponding path on macOS). - **Source Folder for Attaching New Files:** Optionally, choose your system’s Downloads folder (or another folder where new PDFs are saved). - **Automatic Processing:** Check the option to “Automatically Move/Copy Files When Added.” This ensures that any new PDF attached via the Zotero Connector is moved automatically. - **Turn Off Zotero’s PDF Syncing:** If you want all PDFs managed via Google Drive (and not stored in Zotero’s cloud), go to the **Sync** tab in Zotero Preferences and uncheck “Sync attachment files in My Library.” 4. **Set Up Renaming Conventions:** Zotmoov includes renaming functionality, so you can automatically rename your PDFs using a pre-defined naming pattern. To configure this: - **Locate the Renaming Field:** Within the ZotMoov settings (still in the ZotMoov tab under Preferences), look for the option or field related to file renaming. - **Define Your Naming Template:** - Enter your desired renaming pattern using the appropriate wildcards. For example: - `%a` for the author’s last name, - `%y` for the year, - `%t` for the title. - A common pattern might be: - %a_%y_%t - This template renames the file as “AuthorLastname_Year_Title.pdf.” - **Save the Settings:** Once you’ve entered your preferred template, save the changes. From now on, whenever a new PDF is downloaded by Zotero, Zotmoov will automatically move and rename the file according to the pattern you set. _Tip:_ If you ever change the target folder, you can repeat the manual “Move Selected to Directory” process in Zotero to update existing attachments. --- ## Step 4: Use Zotero for Collecting References - **Adding References:** - When adding references using the collector, it will save them into the currently open collection in Zotero. You can use the dropdown feature to save into a particular collection or folder, but it ends up saving in both. - It is easier to select your preferred collection in Zotero before saving. - If you are working on multiple articles, you could set Zotero to a special collection, i.e. "Today's Collection" and then sort all article by collection when finished. - Use your browser connector to add journal articles, books, and other references. Zotero will download the associated PDF (if available) and Zotmoov will automatically move the PDF from Zotero’s default storage to your Google Drive folder. - **Verify File Links:** - In Zotero, each reference with an attachment should now show a linked file (pointing to your Google Drive folder). Files with an attachment will show a ">" in front of the saved article. - You can right-click an attachment and choose “Show File” to confirm its location. --- ## Step 5: Set Up Obsidian for Literature Notes 1. **Install Obsidian:** - Download and install Obsidian from [obsidian.md](https://obsidian.md/). 2. **Create or Open Your Vault:** - Set up a vault where you keep all your academic notes. We will organise this in a later step. For now, just set up the vault and a single folder. 3. **Organize Your Notes:** - Create a dedicated folder for literature notes (for example, “Literature” or “References”). --- ## Step 6: Create an Obsidian Template for Article Metadata Generating the template to work with the Zotero Integration community plugin is not really a job for the inexperienced. Zotero has a range of variables that allow the integration of articles when importing them to Obsidian. An example of a template that will work for this is shown below. You will need to ensure you have the core plugin Templates turned on or the community plugin Templater installed. Alternately, you can watch the video and download a working template [from my website](https://ricraftis.short.gy/Hj1L7b). 1. **Draft Your YAML Template: (If you want to DIY)** - Create a new markdown file (or use your preferred template plugin in Obsidian) with YAML front matter. For example: ```yaml --- title: "{{title}}" authors: "{{authors}}" year: "{{year}}" citekey: "{{citekey}}" pdf_link: "{{pdf_link}}" zotero_link: "{{zotero_link}}" tags: [literature, reference] --- # {{title}} **Authors:** {{authors}} **Year:** {{year}} **Zotero Entry:** [Open in Zotero]({{zotero_link}}) **PDF:** [View PDF]({{pdf_link}}) ## Notes > Add your reflections and analysis here. ``` **Note**: The double-curly-brace placeholders (e.g., `{{title}}`, `{{authors}}`) represent the metadata imported from your Zotero records. You can adapt these variables to match your export format. **Save the Template:** - Place this file in your designated templates folder in Obsidian. If you use the community plugin “Zotero Integration”, configure it to use this template when generating literature notes. --- ## Step 7: Linking PDFs in Obsidian using Symbolic Links To ensure that you can quickly access the full-text PDFs from Obsidian we need to link the vault to the folder in the Google drive. For this to work properly, it is imperative that you DO NOT set up a folder in Obsidian where the linked files will be stored. The reason for this is that the folder in Obsidian will be automatically set up with the commands we use below. - Create a symbolic link (symlink) in your Obsidian vault that points to the Google Drive folder. – On **macOS** or **Linux**, use the terminal command: ```bash ln -s "/path/to/GoogleDrive/Zotero_PDFs" "path/to/your/ObsidianVault/Zotero_PDFs" ``` - On **Windows**, open Command Prompt as administrator and run: ```cmd mklink /D "C:\Path\To\ObsidianVault\Zotero_PDFs" "G:\My Drive\Zotero_PDFs" ``` - If you don't get the syntax correct, you will get an error message. If you are frustrated, paste your commands into an AI model and see what comes up. - Then, in your literature note template, you can refer to the PDF by its relative path (e.g., `[[Zotero_PDFs/SomePaper.pdf]]`). --- ## Step 8: Working with your PDFs First of all, remember that all your PDFs are stored in your Google drive. The symlink mirrors what is in the Google drive. Anything you can access from your Google drive you can also access from the local symlinked drive. When working with PDFs in Obsidian, I would suggest including them in callouts for convenience. There are two ways of doing this: 1\. If you wish to include the full PDF visibly in your Obsidian note, then the syntax is: ``` > [!NOTE] ![[filename of note.pdf]] ``` - This will display the first page of your article and you can then scroll through, select pages and work with it like a PDF. 2\. If you want to include the PDF in the note, but leave it hidden until you need access, then use the following syntax: ``` > [!NOTE]- [[filename of note.pdf]] ``` - The difference in the syntax is the minus (-) sign after the NOTE and then the filename does not have the exclamation (!) mark before the link. - It will result in a callout like the below image: ![[Creating Symbolic Links for Zotero & Obsidian.png]] - Clicking on the > symbol will expand the callout to display its full content: ![[Creating Symbolic Links for Zotero & Obsidian-2.png]] ### Annotating PDFs **While the processing of PDFs in terms of annotation is beyond the scope of this article, it is not a good idea to annotate within the Zotero app using the PDF reader. The reason is that Zotero stores the annotations within its database and if you open the PDF in a different PDF reader, the annotations will not be visible.** **In order to preserve all your annotations, adjust your settings in Zotero to always open PDFs elsewhere. The system default is fine for Mac as it has a native PDF viewer. Windows does not however. I have purchased UPDF which I find the best editor available after trying several.** ![[Creating Symbolic Links for Zotero & Obsidian-3.png]] --- ## Step 8: Using Your New Workflow #### Add New References: - When you add an item using the Zotero Connector, the PDF (if available) is downloaded. - Zotmoov automatically moves the PDF into your Google Drive folder, and Zotero’s attachment links are updated accordingly. #### Generate Literature Notes in Obsidian: - Use your citation integration tool such as Zotero Integration plugin or manually copy metadata from Zotero to create a new literature note using your Obsidian template. - The YAML front matter will capture key details (title, authors, year, etc.) and provide clickable links to both the Zotero record and the PDF. #### Access from Any Device: - Because your PDFs are stored on Google Drive, any device that syncs your Google Drive folder can access them. - Your Obsidian vault (if similarly synced) will let you view and edit notes seamlessly across devices. --- ## Final Thoughts This integrated workflow streamlines your research by connecting three powerful tools: - **Zotero** manages your references. - **Zotmoov** ensures that PDFs are automatically organized and stored on a cloud platform. - **Obsidian** serves as your central workspace for note-taking, enriched with metadata imported via a customizable template. By following these steps, you will create a reliable, cross-device research system that keeps your literature, full texts, and notes perfectly in sync. Enjoy the increased efficiency and accessibility in your academic work! --- ## Any Final Thoughts on the Article? ## Ideas for Future Articles *Link to other notes in Obsidian here perhaps. Use this article to spark ideas for others*