Zotero Obsidian Citations

Adds colored tags to Zotero items that have associated Markdown notes stored in an external folder.
Opens Markdown notes from the contextual menu of Zotero items.

This is an plugin for Zotero, a research source management tool. The ZoteroObsidianCitations plugin searchs an user-defined folder for Markdown files that include a Better BibTeX citekey or Zotero Item Key, and adds a colored tag to the corresponding Zotero items.

Currently this plugin designed with the Obsidian Markdown editor in mind, and was inspired by the obsidian-citation-plugin workflow. It can be adapted to other databases that store Markdown files outside of Zotero, and to other workflows that generate Markdown reading notes linked to Zotero items (such as Zotero's Export Note feature).

Please post any bugs, questions, or feature requests in the Github repository.

Plugin Functions

Adds a colored tag to Zotero items for which there are associated reading notes in an external folder.

Supports multiple Markdown files for a single Zotero item.

Opens an existing Markdown note in Obsidian from the contextual menu of a Zotero item.

Instalation

Download the plugin (the .xpi file) from the latest release: https://github.com/daeh/zotero-obsidian-citations/releases
To download the .xpi file, right click it and select 'Save link as'
Run Zotero (version 5.x or 6.x)
Go to Tools -> Add-ons
Install Add-on From File
Choose the file zotero-obsidian-citations-0.0.15.xpi
Restart Zotero

Setup

A Markdown file can specify which Zotero item it's linked to using either a Better BibTeX citekey or a Zotero-Item-Key.

Link Markdown files to Zotero items using Better BibTeX citekeys.
- This is recommended if you created the Markdown notes with obsidian-citation-plugin.
- The Markdown file names should start with @mycitekey but can include extra information after it (e.g. a reading note might have the file name @shepard1987science.md or @shepard1987science Toward a universal law of generalization for psychological science.md, where shepard1987science is the BetterBibTeX citekey).
Link Markdown files to Zotero items using Zotero Item Keys.
- This is recommended if you created the Markdown notes with the Export Note feature of Zotero.
- The Markdown file contents should include the Zotero-Item-Key in a consistent format (Zotero automatically generates Item Keys; they take the form of ABCD1234, as in zotero://select/library/items/ABCD1234).

NOTE: ZoteroObsidianCitations assumes that a given Markdown file corresponds to a single Zotero item. (A Markdown reading note can reference multiple Zotero items throughout the file, but ZoteroObsidianCitations will only link the Markdown note to one BetterBibTeX-citekey / Zotero-Item-Key.) Multiple Markdown files can point to the same Zotero item.

Option 1: Using BetterBibTeX citekeys

ZoteroObsidianCitations can extract the BetterBibTeX citekey that specifies which Zotero Item a Markdown note corresponds to. The BetterBibTeX citekey can be taken from the Markdown filename or yaml metadata.

In ZoteroObsidianCitations Preferences... (under the Tools menu),
- Specify the location of the folder that contains your Markdown reading notes (e.g. /Users/me/Documents/ObsVault/ReadingNotes/). The ZoteroObsidianCitations plugin will recursively search this path for Markdown files.
  - The default behavior is to search for markdown files beginning with @.
  - Alternatively, you can specify a RegEx pattern to match your reading note files.
- Select the Match notes based on BetterBibTeX citekey option.
  - By default, ZoteroObsidianCitations expects that the filenames of your Markdown reading note files begin with @mycitekey but can include extra information after it (e.g. a reading note might have the file name @shepard1987science.md or @shepard1987science Toward a universal law of generalization for psychological science.md, where shepard1987science is the BetterBibTeX citekey).
- Optionally, you can have ZoteroObsidianCitations read the metadata of your Markdown notes and extract the citekey from one of the fields. To enable this, specify the metadata ID (citekey is a common value).
  - This is necessary if the file names do not begin with the correct citekey, which may happen if the citekeys include special characters (e.g. if a citekey contains :, it will probably need to be taken from the yaml metadata rather than the filename).
Run the synchronization function from Tools -> ZoteroObsidianCitations Sync Tags.
- This will add a tag (ObsCite) to every Zotero item for which there exists a reading note in the external folder you specified.
In the Tags plane of Zotero, right-click on the ObsCite tag and assign it a color, which will mark the tagged items in the preview plane of Zotero.

Option 2: Using Zotero Item Keys

ZoteroObsidianCitations can extract the Zotero-Item-Key that specifies which Zotero Item a Markdown note corresponds to. The Zotero-Item-Key is taken from the Markdown file contents using a custom RegEx pattern.

Zotero automatically generates Item Keys, they take the form of ABCD1234, as in zotero://select/library/items/ABCD1234. NB this is not the same as the BetterBibTeX citekey you assigned an item (e.g. mycitekey in zotero://select/items/@mycitekey).

In ZoteroObsidianCitations Preferences... (under the Tools menu),
- Specify the location of the folder that contains your Markdown reading notes (e.g. /Users/me/Documents/ObsVault/ReadingNotes/). The ZoteroObsidianCitations plugin will recursively search this path for Markdown files.
  - The default behavior is to search for markdown files beginning with @.
  - Alternatively, you can specify a RegEx pattern to match your reading note files.
- Select the Match notes based on Zotero-Item-Key option.
- Specify a RegEx pattern to extract the Zotero-Item-Key from the Markdown contents.
  
  E.g. if your note has the line
  
  - local:: [local zotero](zotero://select/library/items/GZ9DQ2AM)
  
  you could extract the Zotero key (GZ9DQ2AM) using this RegEx pattern:
  
  ^- local::.+\/items\/(\w+)\)
Run the synchronization function from Tools -> ZoteroObsidianCitations Sync Tags.
- This will add a tag (ObsCite) to every Zotero item for which there exists a reading note in the external folder you specified.
In the Tags plane of Zotero, right-click on the ObsCite tag and assign it a color, which will mark the tagged items in the preview plane of Zotero.

Example Markdown Note

In this example Markdown note (@saxe2017emobtom.md), the ZoteroObsidianCitations will use the yaml metadata keyword citekey to find the BetterBibTeX citekey (saxe2017emobtom) to determine which Zotero item to associate with the Markdown file. Notice that the Markdown file can include other BetterBibTeX citekeys and Zotero-Item-Keys, which are ignored by the plugin.

---
citekey: saxe2017emobtom
doi: 10.1016/j.copsyc.2017.04.019
zoterouri: zotero://select/library/items/IACZMXU4
bbturi: zotero://select/items/@saxe2017emobtom
---

# Formalizing emotion concepts within a Bayesian model of theory of mind

[A reference using a Zotero URI](zotero://select/library/items/4RJ97IFL)

[A reference using a BetterBibTeX URI](zotero://select/items/@anzellotti2021opaque)

A reference using an Obsidian wiki link: [[@cusimano2018cogsci]]

Related Projects

obsidian-citation-plugin Obsidian plugin which integrates your academic reference manager with the Obsidian editor.
Zotero 6 Markdown export of notes Zotero's Export Note beta feature.
Zotero-mdnotes A Zotero plugin to export item metadata and notes as Markdown files.
Zotero to Markdown A Python library to retrieve annotations and notes from Zotero and save them into Markdown files.

Notes

GitHub: Source code repository

Code for this extension is based on ZotFile and Zotero Citationcounts (which is based on Zotero DOI Manager, which is based in part on Zotero Google Scholar Citations).

License

Distributed under the MIT License.

cbx812/zotero-obsidian-citations