For academics, PDFs are the lifeblood of research. Articles, books, conference papers; they all land in our folders, heavily annotated and before long, managing them feels like a full-time job. Tools like Zotero and Paperpile help, but annotations are disconnected from notes, thoughts and project management. This makes you miss out on the synergy between notes and annotations. This tutorial is a masterclass on working with PDFs in Obsidian, linking notes and annotations, and using full-text search for PDFs.
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The main benefit we want to achieve is to connect three elements: The PDF annotation + A comment/conclusion from this annotation + the general note on the paper. The PDF and general note on the paper allow you to have “context”, and remember what this paper and annotation were about. Catching up on your notes and their original sources becomes so much more efficient. Take a look at this demo:
Note how I hover the yellow “in”-link to bring up the PDF and hovering the blue source note brings my general notes on the paper. The note itself is stored in a third file called “Demographic rates”. This workflow allows me to store a fact on “Demographic Rates” (which is a topic of my research) but link to the PDF and the paper/source note simultaneously. You can find more info on my note-taking system in this article.
Let’s get started on setting up this workflow:
Importing PDFs in Obsidian
Bringing PDFs into Obsidian is simple, but knowing how to organize them effectively can save you headaches down the line. Obsidian treats PDFs as standard files, so you can drag and drop them into your Vault and link to them like you would any markdown file. There are a few questions to answer:
- Where should I store my PDFs?
I use a __Papers folder to store all PDFs. Use a plugin like Attachment Management to automatically move PDFs to a separate folder. Having all PDFs inside a single folder allows many plugins to work easier with PDFs as they can be identified by the folder. - How should I name PDFs?
I use “Smith 2020” notation. This cite key is up to you but keep it short in order to keep your notes readable when you add multiple links to this paper. - What about Zotero/Paperpile/Mendeley?
After importing PDFs to Obsidian, they are copied (i.e. duplicated) into your vault, and the annotations you made with Zotero are usually lost. I suggest using Zotero only to capture the paper’s metadata, then importing the PDF into Obsidian, working with it there and using Zotero only once you start writing your manuscript in MS Word or Google Docs (which I highly recommend).
Don’t spend too much time thinking about the organization when you start your note-taking journey. The structure will evolve and use.
Editing PDFs in Obsidian
Editing PDFs natively in Obsidian isn’t possible (yet, but it is on the roadmap) without plugins. There are two plugins that bridge the gap: Annotator and PDF++. Both allow you to add highlights, annotations, and links directly in Obsidian. However, the workflows differ:
- Annotator saves annotations in markdown files without modifying PDFs, which are searchable within Obsidian. Links are directed at these annotation files rather than the PDFs.
- PDF++ embeds annotations directly into PDFs, preserving their visual context.
PDF++ is the one I am covering in this article. However, Annotator is great if you need a more lightweight solution that allows you to search through your annotations inside Obsidian.
What are deep links to a PDF?
Imagine you took a note on paper, and some time passed, and you used your notes to write your paper. If your note is stored separately from the paper, you might ask yourself, “Where in the paper did it say this?” so you open the paper and start re-reading it to validate your note’s content. This is not a good use of time.
What if, instead, you could make a highlight in a PDF and link directly to this highlight, then link it to a note summarizing and paraphrasing what you wrote? If you need to look up the question “Where in the paper did it say this?” you just need to click the link. This is efficient and satisfying. But to do this, your notes, PDFs, and annotations need to be part of the same system: Obsidian!
Here is an example of a note where I say that “Ehrlen 2015 use population models to predict extinction debt”. This claim is backed up by a deep link taking me directly into the relevant section of the PDF:
You might notice that the links in my screenshot are different colors. That is because I configured Obsidian with the help of “supercharged links” and “style settings” plugins to display all PDF links in yellow and all source notes in blue rather than the default (green) link colour. You can learn how to do this in-depth as part of my note-taking course, it makes your notes more readable and clear.
Plugin Tutorial: Obsidian PDF++
This plugin allows you to edit PDFs directly inside Obsidian and copy links to the annotations in various formats. It is a fantastic plugin that comes with a lot of settings, making it a little bit daunting. Let’s break it down. Install the Obsidian plugin using Community Plugins → Browse Plugins → PDF++.
Editing PDF files or keeping annotations separate?
The first decision is whether you want your annotations to be permanent inside the PDF. If you send the PDF file to someone, the annotations will be sent along. To enable this, go to settings and check the “Enable PDF editing” box.
If you do not do this, the annotations are stored inside the links to them. Links in Obsidian can contain information like the page, length, and annotation color. See for example, this example:
The yellow link goes to the PDF file but has a few parameters specifying where the annotation is located. If you do not choose to edit the PDF, this link is the only place where the annotation is stored. If you delete the link, the annotation disappears forever as well.
I prefer to keep my highlights inside the PDF rather than the links, but it is a personal choice.
How to use PDF++ in Obsidian
- Select the text that you wish to annotate.
- Pick a format in three parts: Colour, Copy format, and Text format. The combinations of these three define how the link will appear in your notes.
- Paste the copied text into a note after step 2. PDF++ copies the link in the right format, and you need to paste it to wherever you store your notes:
You can customize the copy and text formats in the PDF++ settings. The best format for me I call the “in-link” (discussed in the note-taking course). The in-link format is a structure that links to the specific annotation but also to a source note (which is a note where I keep my general thoughts on the paper). Here is what you need to write into the settings:
Just like Zotero, PDF++ is also capable of annotating images rather than text.
Plugin Tutorial: Obsidian Annotator
Annotator is an older alternative to annotating PDFs in Obsidian. It is, however, much faster and snappier. The highlights are displayed as text-only previews that do not allow you to scroll up and down the PDF. Unfortunately, clicking the annotation link doesn’t always take you to the correct location.
While this plugin works ok, it is not my first choice anymore, and I recommend using PDF++ instead.
Full-text search in PDFs
The OmniSearch plugin allows you to search for PDF content in Obsidian directly. While it works reliably for finding specific terms or jargon, the text-only results can feel a bit cumbersome to navigate. It is a basic plugin that you can use for occasional full-text search. A standalone search app is a better solution if you need full-text search more frequently. Here is how a search for “Heteroblasty” looks in my PDFs:
While OmniSearch finds the right PDFs, it is text-only. To use OmniSearch, you will also need to install a plugin called “Text Extractor”, which extracts the text from the PDFs to allow for extremely fast full-text search.
Full-Text Search in PDFs using Zotero7
The newest Zotero version also features a full-text search for your PDFs. This solution gives identical results to the OmniSearch plugin in Obsidian: Text only. To access it, open the “Advanced Search” and select “Attachment Content” → “contains” → “Your search query…”:
You can access the “Advanced Search” dialogue from the main Menu of Zotero 7.
Full-Text search using AI and PDF Search App
Using PDF Search is a powerful method to search inside PDFs because it shows the preview and locations of the searches and sorts the results by relevance. However, this particular software is only available for Mac OS. Direct the app to search inside the folder containing the PDFs (“__Papers” located inside the vault for me). Here is the result:
The full-text search using the PDF Search app ranks the hits and is generally more convenient tot use.
What is the best PDF plugin for Obsidian?
The best PDF annotation plugin is PDF++, despite its learning curve. Once you understand the logic behind it, it becomes very easy to use and has multiple convenient functions, making it a pleasure to use. For example opening a PDF will usually open it in a split tab and zoom in to a 100%, something you would always do anyways. Annotator is a valid alternative if you want a list of all annotations inside a separate file, however I consider this plugin mostly obsolete.
Note-Taking Course
This workflow is part of the Effortless Note Taking Course, where I will walk you step-by-step through the entire process and explain in more detail what is happening and why this is important. You can get a feel for this in my free version below:
Summary
• Deep-linking PDF annotations, notes, and source references in Obsidian ensure that relevant context is always accessible and reduces the effort of revisiting specific sections or ideas.
• Organize PDFs in a dedicated folder with a consistent naming scheme for compatibility with plugins.
• Use the PDF++ plugin to embed annotations directly into PDFs, preserving the context and enabling precise navigation to specific locations for verification or review.
• The Annotator plugin provides a text-based alternative for storing annotations in markdown files, making them searchable within Obsidian while offering a lightweight workflow.
• Customize link styles to your annotations to make them stand-out using plugins like “Supercharged Links” and “Style Settings”. This improves note readability, organization, especially in complex research projects.
• Full-text search through the OmniSearch plugin supports quick identification of terms within PDFs. It replicates Zotero’s full-text search feature.
• External tools like PDF Search App provide enhanced search functionality with ranked results and visual previews, offering more context for understanding search matches.
- Join the note-taking course for a step-by-step walkthrough and a note-taking system that will transform your research.