# Setting up Zotero Integration for Research Papers and Notes

In this section, the speaker explains how to set up the Zotero integration plugin for research papers and notes.

Installing the Community Plugin

• To get started, you need to install the community plugin.

• Browse for the Zotero integration plugin and install it.

• Make sure to read the documentation and check if there are any additional plugins required.

Configuring Settings

• After installing the plugin, go to options to configure your settings.

• Set up your external PDF utility and choose where you want your notes imported.

• Create a citation command using an output format template that will come into play later when importing notes.

Importing Notes Format

• The settings that govern when importing notes into a file can be found here.

• Use a specific name of command such as "import paper" with a path where the file is located.

• The template portion specifies the title of the paper.

# Highlighting Images in Zotero

In this section, the speaker explains how to highlight images in Zotero and add annotations on those images.

Selecting Images in Zotero

• To select an image in Zotero, use custom screenshot selection tools or square highlights.

• Annotations can be added on selected images by adding comments or tags.

Storing Images in Obsidian

• All highlighted images with annotations will be sent to Obsidian for reusability purposes.

• Reusing these images is possible by referencing them in other papers.

# Organizing PDF Annotations with Zotero and Obsidian

In this section, the speaker explains how to organize PDF annotations using Zotero and Obsidian.

Creating a New Folder for Annotations

• A new folder called "zotero" is created to store the annotations.

• The site key, which is the unique citation key for the paper being extracted, is used as the name of the new folder.

• Images that correlate to notes are stored inside this folder.

Syntax for Image File Names

• If an image cannot be grabbed, the site key will be prepended to the beginning of its file name.

• There is a syntax for page number and x-y coordinates of selected areas in a PDF document. This information can be useful when citing or reusing images.

Automated Organization

• The site key can be used to reference an image.

• The image output path governs where images are stored.

• The template portion "site key" creates a new folder based on what paper is being extracted.

• Extracting notes multiple times does not create duplicates.

Template File

• A single template file contains all notes and content.

• Aliases are used to reference specific notes by name or citation key.

• URLs can also be included in templates.

# Understanding Zotero Metadata and Template Syntax

In this section, the speaker explains how to use metadata tags in Zotero and how to create a template file using nunchucks syntax.

Using Metadata Tags in Zotero

• The paper keywords are the keywords in Zotero.

• Metadata tags are used to pull information into the template using all tags.

• Type status is used for The Supercharged links plugin, while update time on edit plugin is used for updating time on edit.

Creating a Template File with Nunchucks Syntax

• A specific portion of the template file is created for research papers in Zotero to automatically rename them based on the title of the paper.

• The call-out portion of metadata provides a link to the actual PDF of the paper in Zotero.

• The abstract content is dropped into this section for easy access through data view query.

• Related papers defined in Zotero are automatically inserted into this metadata section using nunchucks syntax.

• Data view query searches for information from any note where related metadata contains site key for that particular extracted note by citation key.

Using Visual Aspects in Notes

• General structure of notes is defined along with highlighting scheme which was already present in tag taxonomy note.

• Nunchucks syntax allows more visual aspects to be added to notes such as colors and emojis.

Zotero Integration Plugin

In this section, the speaker explains how to use the Zotero integration plugin and its hotkeys to extract metadata from a paper.

Using the Template

• The speaker defines a template that uses if statements to extract metadata from papers.

• If the annotation has a comment in Zotero, it is extracted into the metadata.

Workflow with Hotkeys

• The speaker has implemented hotkeys for site and import paper using the Zotero integration plugin.

• By pressing option Z or X on Mac (or alt on Windows), an empty note opens up.

• To import a new paper, press option Z to open up a search bar and type in keywords to find the desired paper.

• Selecting a paper will automatically extract all annotations and metadata into an empty note.

Extracted Paper Metadata

• All annotations, related papers, tags, authors, keywords, abstracts are extracted into the note.

• The zotero link is included as well as related data view inline key value pairs.

# Inserting Citations and Related Tags

In this section, the speaker discusses how to insert citations and related tags in notes. They also explain how these tags can be used to see the interconnectedness of notes.

Inserting Citations

• To insert a citation, search for the paper and insert the citation where the cursor is.

• If using citation keys to name papers, it's possible to keep graph relations between papers by making an uncreated note with a link to the site key.

Related Tags

• Using related tags is a powerful way of seeing the interconnectedness of notes.

• The speaker prefers linking ideas and notes together rather than just understanding relationships between papers.

• It's possible to use related data view key-value pairs inside a note and make a link to a site key that doesn't exist yet as a note.

# Best of Both Worlds: Site Key Links and Aliases

In this section, the speaker explains how they found a way to use site key links while still using their approach.

Using Aliases

• Put the site key and make an alias for it so that when importing papers again, both links will exist.

• When renaming files using syntax in templates, set initial output path inbox site key in Zotero import settings so that file names match aliases.

Results

• The link exists when importing papers again using this new setup.

• The graph link exists even though data view query isn't picking it up.

# Setting up Jinja file

In this section, the speaker explains how to set up a Jinja file and ensure that the Alias is related to itself.

Renaming Files

• The speaker renames the file automatically by creating it in a certain way.

• The Alias is related to itself so that it can be extracted dynamically.

Extracting Papers

• Extracted papers will show anything that was linking to them.

• When extracting papers, they will automatically rename themselves and show backlinks.

Using Links in Graph

• Links exist in the graph but also show anything that links to that paper.

• This method allows for both links and metadata without all the linking in the graph.

# Data View Query

In this section, the speaker discusses how data view queries work with Jinja templates.

Displaying Site Key

• The data view query displays the exact name of the file based on all template syntax used.

• The site key is displayed using an Alias within Jinja.

# Note Taking Workflow

In this section, the speaker explains their note-taking workflow using bullet points and block references.

Bullet Points for Notes

• Speaker uses bullet points for notes as sub-bullets make it easier to do block references.

• Annotations leave spaces between child items which can be easily fixed with backspacing.

Highlighter Plugin

• Speaker uses the highlighter plugin which uses Mark HTML tags and CSS to target the highlighter color class.

# Zotero Integration Plugin

In this section, the speaker talks about how they use the Zotero integration plugin to extract content and define annotation color categories.

Using Existing Infrastructure

• The speaker uses the Mark class highlighter Dash and the annotation color category from Zotero.

• The name of the color on the highlight is automatically dropped into Obsidian, so there is no need to define it manually.

Workflow for Literature Notes

• The speaker only does extractions once to avoid constant resyncing.

• This literature note will be used forevermore.

• If new content needs to be added, a re-extraction is done and then added to the older literature note.

Benefits of Using Zotero Integration Plugin

• It's super convenient and gives back all functionality expected from MD notes and file plugins.

• It's easier to set up, configure, and use than expected.

• Penny Hatcher did a great video on it that helped the speaker dive right in.

# Color Scheme for Note-Taking

In this section, the speaker discusses their taxonomy for note-taking using colors.

Importance of Highlight Colors

• Highlight colors correlate with what is being done in Zotero.

• They also correlate with flag colors used when taking notes on books or research papers.

Standard Operating Model

• The same color scheme is used across all paradigms for taking notes (books, research papers).

• This allows for a standard operating model that can be worked off of.

Book Tabs

• The speaker found book tabs in good enough Groovebox colors.

• They will post Amazon affiliate links to these products in the description of the pin comment.

# Conclusion

In this section, the speaker concludes by summarizing their standard operating model for research paper notes and discussing their plans for processing notes on a book they recently read.

Standard Operating Model

• The speaker's workflow involves using the Zotero integration plugin to extract content and define annotation color categories.

• They only do extractions once to avoid constant resyncing.

• A literature note is created that will be used forevermore.

• New content is added by re-extracting and then adding it to the older literature note.

Plans for Processing Notes

• The speaker has at least 200 more papers to potentially go through based on a book they recently read.

• They use a taxonomy for note-taking using colors that allows them to work off of a standard operating model across all paradigms (books, research papers).

• Book tabs in good enough Groovebox colors were found and will be posted as Amazon affiliate links.