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
• Open Zotero (version 7.x)
• From Tools -> Plugins
• Select Install Add-on From File... from the gear icon ⛭
• Choose the .xpi file you downloaded (e.g. markdb-connect.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.

configuration details

• In Zotero's Settings, click the MarkDB-Connect preference pane.

  • Specify the location of the folder that contains your markdown reading notes (e.g. /Users/me/Documents/ObsVault/ReadingNotes/). The MarkDB-Connect plugin will recursively search this path for markdown files.

  • By default, MarkDB-Connect 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 with the BetterBibTeX citekey shepard1987science could have the filename @shepard1987science.md or @shepard1987science Toward a universal law of generalization for psychological science.md).

    • If your BetterBibTeX citekeys contain certain special characters (e.g. :, /), you will need to extract the citekeys from the markdown file's contents rather than its filename.

  • If the default does not match your use case, you can specify how to extract BetterBibTeX citekeys.

    • A. filename - Select Custom File Filter and define a RegExp with a single capturing group.

      • E.g. the default is ^@(\S+).*\.md$, which looks for files beginning with @ and uses the first word as the BetterBibTeX citekey.

    • B. metadata - Select BetterBibTeX citekey - taken from YAML metadata and specify a keyword from the notes' YAML frontmatter (here's an example).

      • For info on metadata syntax, see YAML front matter.

    • C. contents - Select BetterBibTeX citekey - captured with custom RegExp and define a RegExp with a single capturing group to return exactly 1 match per file.

• Run the synchronization function from Tools -> MarkDB-Connect 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. (In the screenshot above, Zotero items associated with reading notes are marked with a 🟦 blue tag.)

---

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).

configuration details

• In Zotero's Settings, click the MarkDB-Connect preference pane.

  • Specify the location of the folder that contains your markdown reading notes (e.g. /Users/me/Documents/ObsVault/ReadingNotes/). The MarkDB-Connect plugin will recursively search this path for markdown files.

    • The default behavior is to search for markdown files beginning with @.

    • Alternatively, you can define a custom RegExp pattern to match your reading note files.

  • Select the Match Markdown Files to Zotero Items Using: Zotero-Item-Key - captured with custom RegExp option.

  • Specify a RegExp 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 RegExp pattern:

    ^- local::.+\/items\/(\w+)\)

• Run the synchronization function from Tools -> MarkDB-Connect 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. (In the screenshot above, Zotero items associated with reading notes are marked with a 🟦 blue tag.)

---

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
---

# @saxe2017emobtom

**Formalizing emotion concepts within a Bayesian model of theory of mind**
(2017) _Current Opinion in Psychology_
[Open in Zotero](zotero://select/library/items/IACZMXU4)

The body of notes can include references to other Zotero items.
The _MarkDB-Connect_ plugin will only link this file to one Zotero item
(in this case, it will use the value of the `citekey` property).

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]]

Example Templates

Below are example templates for various Obsidian plugins

Template for obsidian-citation-plugin

---
citekey: "{{citekey}}"
title: "{{title}}"
year: {{year}}
authors: [{{authorString}}]
{{#if containerTitle~}} publication: "{{containerTitle}}" {{~else~}} {{~/if}}
{{#if DOI~}} doi: "{{DOI}}" {{~else~}} {{~/if}}
aliases: ["@{{citekey}}", "@{{citekey}} {{title}}"]
tags: 
 - readingNote
---

# @{{citekey}}

**{{title}}**
{{authorString}}
{{#if year~}} ({{year}}) {{~else~}} {{~/if}} {{~#if containerTitle}} _{{containerTitle~}}_ {{~else~}} {{~/if}}
[Open in Zotero]({{zoteroSelectURI}})

Template for ZotLit

Make a file (e.g. zotlit-properties.eta.md) with the following contents, and point to that file in ZotLit settings: Template > Note Properties.

citekey: "<%= it.citekey %>"
title: "<%= it.title %>"
<% if (it.date) { %>year: <%= it.date %><% } %>
authors: [<%= it.authors.map(v => v.firstName v.lastName) %>]
<% if (it.publicationTitle) { %>publication: "<%= it.publicationTitle %>"<% } %>
<% if (it.DOI) { %>doi: "<%= it.DOI %>"<% } %>
aliases: ["@<%= it.citekey %>", "@<%= it.citekey %> <%= it.title %>"]
tags:
 - readingNote

Suppressing the Zotero security notification

Recent builds of Zotero have introduced a security notification for external links. At present, Zotero does not remember the user's link preferences, so this alert is shown every time an application-specific URI is launched. You can suppress this warning by setting security.external_protocol_requires_permission to false in Zotero's advanced configuration.

Instructions for modifying Zotero's advanced config

1. Open Zotero Settings
2. Click the "Advanced" tab
3. Click the "Config Editor" button
4. Click the "Accept Risk and Continue" button
5. Search for security.external_protocol_requires_permission
6. Double click the security.external_protocol_requires_permission item to toggle its value to false

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