zotero-markdb-connect

• 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 citation key shepard1987science could have the filename @shepard1987science.md or @shepard1987science Toward a universal law of generalization for psychological science.md).

    • If your citation keys 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 citation keys.

    • 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 citation key.

    • B. metadata - Select Citation key - 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 Citation key - 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.)

• 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.)

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}})

Example for ZotLit v2

ZotLit v2 uses managed frontmatter fields, not a Note Properties Eta file. In Obsidian’s Settings > ZotLit > Templates > Frontmatter, keep (or restore) the default citekey field:

• Key: citekey
• Expression: zt.citationKey (without {{ }})
• Language: Liquid
• Merge strategy: Replace

Use an item with a nonempty, filename-safe, whitespace-free citation key (for example, saxe2017emobtom). ZotLit writes citekey: null for an item without a citation key; that cannot identify an item using MarkDB-Connect’s citation-key mode.

To keep MarkDB-Connect’s default @ filename filter, create an editable Note filename template under Settings > ZotLit > Templates. In zotlit-filename.liquid.md, use:

@{{ zt.citationKey }}{% suffix %}

ZotLit appends .md automatically; suffix handles filename collisions. Keep the template folder outside the folder MarkDB-Connect scans, and set that scan folder to your literature notes folder. In MarkDB-Connect, select Citation key - taken from YAML metadata and set the keyword to citekey. This also works for suffixed filenames because the key comes from frontmatter, not the filename.

For example, a note named @saxe2017emobtom.md will contain this property (alongside ZotLit’s other frontmatter):

citekey: saxe2017emobtom

Optional metadata can also be configured as Liquid fields with Replace: title → zt.title (already a default), authors → zt.authors | map: "fullName", year → zt.date.year, publication → zt.containerTitle, and doi → zt.DOI. These expressions return typed values; ZotLit handles YAML serialization, including quoting and author arrays. No JavaScript Templates opt-in is needed for this example.

For existing notes, ZotLit’s Update literature note metadata command refreshes managed frontmatter without replacing the note body. Then run MarkDB-Connect Sync Tags in Zotero as described above. This example only configures note matching; see ZotLit’s v1 template migration guide for migrating other templates.

The dialog can be bypassed on a per-scheme basis by creating a network.protocol-handler.external.<scheme> preference set to true. The setting must be added manually (it does not exist by default).

1. Open Zotero Settings
2. Click the “Advanced” tab
3. Click the “Config Editor” button
4. Click the “Accept Risk and Continue” button
5. In the search field, enter the config you want to create, e.g.
   • network.protocol-handler.external.obsidian
   • network.protocol-handler.external.logseq
6. If no matching entry appears, click the “+” (New) button on the right of the novel config.
   • Make sure the type is boolean and the value is true. By default, the setting should be set to “Boolean” and should be assigned true when created.
   • 

If prompts still appear for links triggered from outside Zotero, you can additionally set network.protocol-handler.prompt-from-external to false using the same procedure.

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