# Deep Sit plugin for Obsidian ## Deep Sit Deep Sit is an Obsidian plugin that allows you to easily cite and refer to the literature stored in your Reference Manager Library (Zotero) during your note-taking. This integration enhances the use of Obsidian as a focused study and research tool. ## Requirements - Zotero (version 7). (https://www.zotero.org/download/) - Zotero's Better BibTeX plugin. (https://retorque.re/zotero-better-bibtex/index.html) - Note: Zotero, with Better BibTeX installed, must be running while you are using this plugin. ## Screenshots - Cite as you write ![Citing](/screenshots/citing.png) - References ![References](/screenshots/references.png) - Annotations ![Annotations](/screenshots/annotations.png) - Insert References Section ![References Section](/screenshots/references_section.png) ## Installation ### Installation through Obsidian's official Community plugins channel (Recommended) Deep Sit has been accepted to Obsidian's official Community plugins channel in December 2025. Please install according to the Obsidian Help documentation: https://help.obsidian.md/community-plugins ### Manual installation - Go to the Releases page of the plugin https://github.com/bassio/obsidian-deepsit/releases and choose a release to download. - Download main.js, styles.css, manifest.json files from the "Assets" of the release. - Open your vault's plugins folder (VaultFolder/.obsidian/plugins) and create a new folder there named obsidian-deepsit. - Copy over main.js, styles.css, manifest.json to the newly-created folder "VaultFolder/.obsidian/plugins/obsidien-deepsit/". ### BRAT - Another option for installation is to trial the the Beta Reviewers Auto-update Tester (BRAT) plugin (https://github.com/TfTHacker/obsidian42-brat), which is available through the Obsidian Community plugins and enable it. - Go to the BRAT plugin settings and select the Add beta plugin button. - Add Deep Sit via pasting its repository link: https://github.com/bassio/obsidian-deepsit and click the Add Plugin button. ## Use case This plugin's would fit optimally within your research workflow, if you operate using the following assumptions: - You use zotero as your main reference manager. - You have a large zotero library with potentially many hundreds of pdf articles, and you use zotero for in-pdf annotations/highlights. - You aim to write your own study and/or research notes / articles (e.g. a "Zettelkasten" or a "Second Brain" system, or alternatively exam study curriculum) - You would have wished to keep your notes and study and/or research writings within Zotero as well for optimal integration, but unfortunately you find that you need a more powerful and flexible tool for your note-taking (i.e. Obsidian). - You want to be able to, in your notes, to easily and quickly reference / cite the relevant literature. - You want to be able to easily review or peek into your highlighted or annotated source references. ## Features ### Citation features - Tie a markdown note to a "Zotero collection" of references using the "bib" keyword in the yaml frontmatter. - In-text citations using the gold-standard "[@reference]" pandoc citation syntax. See https://pandoc.org/demo/example33/8.20-citation-syntax.html#citation-syntax - Automatic reference selection pop-up dropbox for easy citations. ### Reference list features - Keep track of your cited references, in an *ordered* Reference List, easily visible on the right side of your workspace (References mode). - A "Refresh button" to allow you to refresh your References list as you add new / delete citations within your markdown or for when you add new items to Zotero. - The "Bibliography mode" allows you to alternatively list all the References in the accompanying Zotero collection for quick reference. - Choose a default of References View Mode versus Bibliography View Mode (via Plugin Settings). - Automatic highlighting of references with pdf attachments and One-click jump to the pdf in your Zotero Library. - Insert "References" in the note's text via context menu. ### Annotation features - Easily keep track of which references in your Bibliography has annotations. - Efficient "Multi-annotation" feature: View all annotations for all pdf files within a Zotero collection in one view pane. - Review Annotations within a pop-up modal or within the plugin view pane. (via Plugin Settings) - Icons for quick-jump to the annotation in Zotero and for quick-copy the appropriately-referenced annotation to clipboard. - Annotations view also includes Zotero "area" pdf annotations viewed as in-line pictures. ## Usage - Once the plugin is installed and enabled, an icon (a graduation cap icon) will appear on the right sided leaf (sidebar) in Obsidian's workspace. - Clicking on the icon will bring Deep Sit's references into view in the right sidebar. - To start citing references from your Zotero in an Obsidian note, add to the note's YAML frontmatter (also called in Obsidian note "Properties") a property called **bib**, and enter the path to the Zotero collection you want to be referencing as the underlying bibliography for this note. - The path to the Zotero collection should include the name of the Zotero library first, then use forward slashes for every subcollection. For example: *My Library*/My Papers/paper1. - Please make sure that Zotero is running with the Better Bibtex plugin activated for active communication with the Obsidian Deep Sit plugin. - Click the refresh button in Deep Sit's View to refresh the note's bibliography. - Cite while you write, using the "[@citekey]" pandoc citation syntax, and an autocomplete pop-up should appear to help you choose your reference, based on the item's *Citation key* in Zotero. (Refer to Zotero Better Bibtex documentation if you are not sure what is an item's citekey is.) - Click the refresh button to refresh the reference list in Deep Sit's View. ## Disclosures As of October 2025, this plugin does *not* contain: - [x] payments - [x] account requirements - [x] network use - [x] external file access - [x] ads - [x] telemetry with privacy policy - [x] closed source code ## Acknowledgements - Emiliano Heyns for the excellent Zotero Better BibTeX plugin. (https://retorque.re/zotero-better-bibtex/index.html) - CSS only spinner obtained from https://github.com/vineethtrv/css-loader (MIT © 2020 Vineeth.TR). - Flexoki colour scheme (MIT © Steph Ango; https://stephango.com/flexoki)