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-**_Adds colored tags to Zotero items that have associated Markdown notes stored in an external folder._**
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-**_Opens Markdown notes from the contextual menu of Zotero items._**
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-**_Scans your Markdown database and adds a colored tag to associated Zotero items._**
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-**_Jump to Markdown notes from the contextual menu of Zotero items._**
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-**_Supports various Markdown databases, including [Obsidian](https://obsidian.md), [logseq](https://logseq.com), and [Zettlr](https://www.zettlr.com)_**
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 ZoteroItemKey, and adds a colored tag to the corresponding Zotero items.
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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.
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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).
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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).
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Please post any bugs, questions, or feature requests in the Github repository.
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## Plugin Functions
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Adds a colored tag to Zotero items for which there are associated reading notes in an external folder.
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Supports multiple Markdown files for a single Zotero item.
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Supports multiple markdown files for a single Zotero item.
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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.
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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.
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## Setup
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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.
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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.
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1.Link Markdown files to Zotero items using **Better BibTeX citekeys**.
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1.Using **Better BibTeX citekeys** to link markdown files to Zotero items.
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- This is recommended if you created the Markdown notes with [obsidian-citation-plugin](https://github.com/hans/obsidian-citation-plugin).
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- This is recommended if you created the markdown notes with [obsidian-citation-plugin](https://github.com/hans/obsidian-citation-plugin).
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- The BetterBibTeX citekey needs to appear in the filename or the metadata of the Markdown note.
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- The BetterBibTeX citekey needs to appear in the filename or the metadata of the markdown note.
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2.Link Markdown files to Zotero items using **Zotero Item Keys**.
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2.Using **Zotero Item Keys** to link markdown files to Zotero items.
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- This is recommended if you created the Markdown notes with the `Export Note` feature of Zotero.
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- The Markdown note contents should include the Zotero-Item-Key in a consistent format.
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- This is recommended if you created the markdown notes with the `Export Note` feature of Zotero.
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- The markdown note contents should include the Zotero-Item-Key in a consistent format.
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NOTE: Multiple Markdown files can point to the same Zotero item. However, _MarkDB-Connect_ assumes that a given Markdown file corresponds 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.)
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NOTE: multiple markdown files can point to the same Zotero item. However, _MarkDB-Connect_ assumes that a given markdown file corresponds 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.)
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---
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### Option 1: Using BetterBibTeX citekeys
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_MarkDB-Connect_ can extract the BetterBibTeX citekey that specifies which Zotero Item a Markdown note corresponds to. The BetterBibTeX citekey can be taken from the Markdown filename or yaml metadata.
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_MarkDB-Connect_ can extract the BetterBibTeX citekey that specifies which Zotero Item a markdown note corresponds to. The BetterBibTeX citekey can be taken from the markdown filename or yaml metadata.
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- In `MarkDBConnect Preferences...` (under the `Tools` menu),
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- 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.
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- 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.
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- The default behavior is to search for markdown files beginning with `@`.
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- Alternatively, you can specify a RegEx pattern to match your reading note files.
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- Select the `Match notes based on BetterBibTeX citekey` option.
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- 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 file name `@shepard1987science.md` or `@shepard1987science Toward a universal law of generalization for psychological science.md`).
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- 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 file name `@shepard1987science.md` or `@shepard1987science Toward a universal law of generalization for psychological science.md`).
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- Optionally, you can have _MarkDB-Connect_ read the metadata of your Markdown notes and extract the citekey from one of the fields. To enable this, specify the metadata ID (`citekey` is a common value).
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- Optionally, you can have _MarkDB-Connect_ read the metadata of your markdown notes and extract the citekey from one of the fields. To enable this, specify the metadata ID (`citekey` is a common value).
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- This is necessary if the file names do not begin with the correct citekey, which may happen if the citekeys include special characters (e.g. if a citekey contains `:`, it will probably need to be taken from the yaml metadata rather than the filename).
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### Option 2: Using Zotero Item Keys
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_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 RegEx pattern.
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_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 RegEx pattern.
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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`).
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- In `MarkDBConnect Preferences...` (under the `Tools` menu),
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- 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.
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- 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.
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- The default behavior is to search for markdown files beginning with `@`.
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- Alternatively, you can specify a RegEx pattern to match your reading note files.
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- Select the `Match notes based on Zotero-Item-Key` option.
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- Specify a RegEx pattern to extract the Zotero-Item-Key from the Markdown contents.
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- Specify a RegEx pattern to extract the Zotero-Item-Key from the markdown contents.
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E.g. if your note has the line
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## Example Markdown Note
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In this example Markdown note (`@saxe2017emobtom.md`), the _MarkDB-Connect_ will use the yaml metadata keyword `citekey` to find the BetterBibTeX citekey (`saxe2017emobtom`) to determine 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.
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In this example markdown note (`@saxe2017emobtom.md`), the _MarkDB-Connect_ will use the yaml metadata keyword `citekey` to find the BetterBibTeX citekey (`saxe2017emobtom`) to determine 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.
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```markdown
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citekey: saxe2017emobtom
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doi: 10.1016/j.copsyc.2017.04.019
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zoterouri: zotero://select/library/items/IACZMXU4
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bbturi: zotero://select/items/@saxe2017emobtom
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doi: 10.1016/j.copsyc.2017.04.019
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---
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# Formalizing emotion concepts within a Bayesian model of theory of mind
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[A reference using a Zotero URI](zotero://select/library/items/4RJ97IFL)
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[A reference to another paper using a Zotero URI](zotero://select/library/items/4RJ97IFL)
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[A reference using a BetterBibTeX URI](zotero://select/items/@anzellotti2021opaque)
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[A reference to another paper using a BetterBibTeX URI](zotero://select/items/@anzellotti2021opaque)
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A reference using an Obsidian wiki link: [[@cusimano2018cogsci]]
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A reference to another paper using an Obsidian wiki link: [[@cusimano2018cogsci]]
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