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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

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.2%) to scientific vocabulary

Keywords

bibliography logseq markdown obsidian obsidian-md zettlr zotero zotero-plugin

Keywords from Contributors

mesh interpretability sequences projection interactive optim hacking network-simulation
Last synced: 6 months ago · JSON representation

Repository

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.

Basic Info
  • Host: GitHub
  • Owner: daeh
  • License: mit
  • Language: TypeScript
  • Default Branch: main
  • Homepage:
  • Size: 2.15 MB
Statistics
  • Stars: 565
  • Watchers: 8
  • Forks: 8
  • Open Issues: 8
  • Releases: 49
Topics
bibliography logseq markdown obsidian obsidian-md zettlr zotero zotero-plugin
Created about 4 years ago · Last pushed 10 months ago
Metadata Files
Readme License Zenodo

README.md

GitHub release (latest by date) GitHub Downloads all releases GitHub Downloads (latest release)

MarkDB-Connect (Zotero Markdown DataBase Connect)

zotero target version Using 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, logseq, and Zettlr
  • [Zotero 7](https://www.zotero.org/support/betabuilds) compatible_

MarkDBConnectScreenshot

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.
  1. 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](#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 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

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:

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.

Zotero Security Notification

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

Notes

GitHub: Source code repository

This extension uses the zotero-plugin-template.

License

Distributed under the MIT License.

Author

Personal Website BlueSky

Owner

  • Name: Dae
  • Login: daeh
  • Kind: user
  • Location: Cambridge, MA
  • Company: MIT

Neukom Computational Science Postdoc Fellow at Dartmouth. PhD from MIT Brain and Cognitive Sciences.

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Last synced: 9 months ago

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