MarkDB-Connect (Zotero Markdown DataBase Connect)

• Scans your Markdown database and adds a colored tag to associated Zotero items.
• Jump to Markdown notes from the contextual menu of Zotero items.
• Supports various Markdown databases, including Obsidian, logseq, and Zettlr
• Zotero 7 compatible

This is a plugin for Zotero, a research source management tool. The MarkDB-Connect plugin searches a 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.

This plugin was initially designed with the Obsidian markdown editor in mind, and was inspired by the obsidian-citation-plugin workflow. It offers preliminary support for logseq and Zettlr. 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's issues.

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, logseq, or the system's default markdown note editor (e.g. Zettlr, Typora) from the contextual menu of a Zotero item.

Installation

• Download the plugin (the .xpi file) from the latest release, v0.1.0
• Open Zotero (version 7.x)
• From Tools -> Add-ons
• Select Install Add-on From File... from the gear icon ⛭
• Choose the .xpi file you downloaded (e.g. markdb-connect-0.1.0.xpi)
• Restart Zotero

[!NOTE] Beginning with v0.1.0, MarkDB-Connect will support Zotero 7 exclusively. The last release for Zotero 6 is v0.0.27.

Setup

A markdown file can specify which Zotero item it's linked to using either a Better BibTeX citekey or a Zotero-Item-Key. I recommend using Better BibTeX citekeys when possible.

1. Using Better BibTeX citekeys to link markdown files to Zotero items.

   • This is recommended if you created the markdown notes with obsidian-citation-plugin, BibNotes Formatter, or Obsidian Zotero Integration.

   • The BetterBibTeX citekey can be taken from the filename, YAML metadata, or body of the markdown note.

   • FYI There's a nice configuration tutorial detailing a common use case (thanks to Prof. Elena Razlogova).

2. Using Zotero Item Keys to link markdown files to Zotero items.

   • This is recommended if you created the markdown notes with the Export Note feature of Zotero.

   • The markdown note contents should include the Zotero-Item-Key in a consistent format.

NOTE: multiple markdown files can point to the same Zotero item. But a given markdown file should only be linked to a single Zotero item. A markdown reading note can reference multiple Zotero items throughout the file, but MarkDB-Connect will only link the markdown note to one BetterBibTeX-citekey / Zotero-Item-Key.

Option 1: Using BetterBibTeX citekeys

MarkDB-Connect can extract the BetterBibTeX citekey that specifies which Zotero Item a markdown note corresponds to. The BetterBibTeX citekey can be taken from a markdown file's filename, YAML metadata, or elsewhere in the file's contents.

Option 2: Using Zotero Item Keys

MarkDB-Connect 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 RegExp 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).

Example Markdown Note

In this example markdown note (@saxe2017emobtom.md), MarkDB-Connect will use the YAML metadata keyword citekey to find the BetterBibTeX citekey (saxe2017emobtom) that determines 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
zoterouri: zotero://select/library/items/IACZMXU4
bbturi: zotero://select/items/@saxe2017emobtom
doi: 10.1016/j.copsyc.2017.04.019
---

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

The body of notes can include references to other Zotero items. The _MarkDB-Connect_ plugin
will only link this file to one Zotero item.

Here are links to other papers.

This one uses [a Zotero URI](zotero://select/library/items/4RJ97IFL)

This one uses [a BetterBibTeX URI](zotero://select/items/@anzellotti2021opaque)

This one uses an Obsidian wiki link: [[@cusimano2018cogsci]]

Related Projects

• obsidian-citation-plugin by hans
  • Obsidian plugin that integrates your Zotero database with Obsidian.
• BibNotes Formatter by stefanopagliari
  • Obsidian plugin to facilitate exporting annotations from Zotero into Obsidian.
• Obsidian Zotero Integration by mgmeyers
  • Obsidian plugin to facilitate exporting annotations from Zotero into Obsidian.
• Zotero 6 'Export Notes' feature by Zotero
  • Zotero 6 beta feature to export notes and annotations from Zotero items as markdown files.
• Zotero-mdnotes by argenos
  • Zotero plugin to export metadata and notes from Zotero items as markdown files.
• Zotero to Markdown by e-alizadeh
  • Python library to export annotations and notes from Zotero items as markdown files.
• Zotero Better Notes by windingwind
  • A Zotero plugin for note management.
• Logseq Citations Plugin by sawhney17
  • Logseq plugin that integrates your Zotero database with Logseq.

Notes

GitHub: Source code repository

This extension uses the zotero-plugin-template.

License

Distributed under the MIT License.

Author