Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/daeh/zotero-markdb-connect
Zotero plugin that links your Markdown database to Zotero. Jump directly from Zotero Items to connected Markdown files. Automatically tags Zotero Items so you can easily see which papers you've made notes for.
https://github.com/daeh/zotero-markdb-connect
bibliography logseq markdown obsidian obsidian-md zettlr zotero zotero-plugin
Last synced: about 10 hours ago
JSON representation
Zotero plugin that links your Markdown database to Zotero. Jump directly from Zotero Items to connected Markdown files. Automatically tags Zotero Items so you can easily see which papers you've made notes for.
- Host: GitHub
- URL: https://github.com/daeh/zotero-markdb-connect
- Owner: daeh
- License: mit
- Created: 2021-12-27T21:15:59.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-11-04T21:46:32.000Z (2 months ago)
- Last Synced: 2025-01-04T17:06:24.842Z (7 days ago)
- Topics: bibliography, logseq, markdown, obsidian, obsidian-md, zettlr, zotero, zotero-plugin
- Language: TypeScript
- Homepage:
- Size: 1.98 MB
- Stars: 534
- Watchers: 8
- Forks: 8
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - daeh/zotero-markdb-connect - Zotero plugin that links your Markdown database to Zotero. Jump directly from Zotero Items to connected Markdown files. Automatically tags Zotero Items so you can easily see which papers you've made n (TypeScript)
- awesome-zotero - Zotero-markdb-connect - Zotero plugin that links your Markdown database to Zotero. (Extensions / Productivity)
- awesome-zotero - Zotero-markdb-connect - Zotero plugin that links your Markdown database to Zotero. (Extensions / Productivity)
README
[](https://github.com/daeh/zotero-markdb-connect/releases/latest) [](https://github.com/daeh/zotero-markdb-connect/releases/latest) [](https://github.com/daeh/zotero-markdb-connect/releases/latest)
# MarkDB-Connect (Zotero Markdown DataBase Connect)
[](https://www.zotero.org) [](https://github.com/windingwind/zotero-plugin-template)
- **_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](https://obsidian.md), [logseq](https://logseq.com), and [Zettlr](https://www.zettlr.com)_**
- **_[Zotero 7](https://www.zotero.org/support/beta_builds) compatible_**
This is a plugin for [Zotero](https://www.zotero.org), a research source management tool. The _MarkDB-Connect_ plugin searches a user-defined folder for markdown files that include a [Better BibTeX](https://retorque.re/zotero-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](https://obsidian.md) markdown editor in mind, and was inspired by the [obsidian-citation-plugin](https://github.com/hans/obsidian-citation-plugin) workflow. It offers preliminary support for [logseq](https://logseq.com) and [Zettlr](https://www.zettlr.com). 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](https://github.com/daeh/zotero-markdb-connect/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc).
## 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](https://obsidian.md), [logseq](https://logseq.com), or the system's default markdown note editor (e.g. [Zettlr](https://www.zettlr.com), [Typora](https://typora.io)) from the contextual menu of a Zotero item.
## Installation
- Download the plugin (the `.xpi` file) from the [latest release](https://github.com/daeh/zotero-markdb-connect/releases/latest)
- 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`](https://github.com/daeh/zotero-markdb-connect/releases/tag/v0.0.27).
## Setup
A markdown file can specify which Zotero item it's linked to using either a [Better BibTeX](https://retorque.re/zotero-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](https://github.com/hans/obsidian-citation-plugin), [BibNotes Formatter](https://github.com/stefanopagliari/bibnotes), or [Obsidian Zotero Integration](https://github.com/mgmeyers/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](https://publish.obsidian.md/history-notes/Option+-+Link+from+a+Zotero+item+back+to+related+notes+in+Obsidian) 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](https://help.obsidian.md/Advanced+topics/YAML+front+matter), 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](#example-markdown-note)).
- For info on metadata syntax, see [YAML front matter](https://help.obsidian.md/Advanced+topics/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](https://help.obsidian.md/Advanced+topics/YAML+front+matter) 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.
```markdown
---
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](https://github.com/hans/obsidian-citation-plugin)
```md
---
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`.
```eta
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](https://github.com/hans/obsidian-citation-plugin) by hans
- Obsidian plugin that integrates your Zotero database with Obsidian.
- [BibNotes Formatter](https://github.com/stefanopagliari/bibnotes) by stefanopagliari
- Obsidian plugin to facilitate exporting annotations from Zotero into Obsidian.
- [Obsidian Zotero Integration](https://github.com/mgmeyers/obsidian-zotero-integration) by mgmeyers
- Obsidian plugin to facilitate exporting annotations from Zotero into Obsidian.
- [Zotero 6 'Export Notes' feature](https://forums.zotero.org/discussion/93521/available-for-beta-testing-markdown-export-of-notes/p1) by Zotero
- Zotero 6 beta feature to export notes and annotations from Zotero items as markdown files.
- [Zotero-mdnotes](https://argentinaos.com/zotero-mdnotes/) by argenos
- Zotero plugin to export metadata and notes from Zotero items as markdown files.
- [Zotero to Markdown](https://github.com/e-alizadeh/Zotero2md) by e-alizadeh
- Python library to export annotations and notes from Zotero items as markdown files.
- [Zotero Better Notes](https://github.com/windingwind/zotero-better-notes) by windingwind
- A Zotero plugin for note management.
- [Logseq Citations Plugin](https://github.com/sawhney17/logseq-citation-manager) by sawhney17
- Logseq plugin that integrates your Zotero database with Logseq.
## Notes
[GitHub](https://github.com/daeh/zotero-markdb-connect): Source code repository
This extension uses the [zotero-plugin-template](https://github.com/windingwind/zotero-plugin-template).
## License
Distributed under the MIT License.
## Author
[](https://daeh.info) [](https://bsky.app/profile/dae.bsky.social) [](https://x.com/DaeHoulihan)