---
title: Zotero 101
author: argentum
date: 2021-04-24
---
# Why do you need a reference manager?
---
## Do you...
- publicly share your notes or content derived from your notes?
- care about the provenance of your ideas?
::: notes
If I could summarize the survey in two main use cases, sharing vs your own notes.
The main thing is you want to keep track of the provenance of your ideas:
1. For yourself, you want to know where an idea originated from.
2. If you share your notes or the output derived from them, you want to properly attribute works or cite authors of the ideas that inspired you or that you're agreeing with or criticizing
3. If you want to share the original source of something that inspired an idea for you
4. Tracing back errors or misunderstandings
5. Starting point for a literature search with tools like connected papers or research rabbit
:::
---
### How does it help?
- Unique IDs
- Searching/Indexing
- Automating the formatting of citations
::: notes
- Pandoc plugin doesn't support citations as of 2021-04-18
- Command: `pandoc -s vault/Pandoc\ demo.md --bibliography vault/H2G2.bib --citeproc -o vault/H2G2.pdf `
- Style: `pandoc -s vault/Pandoc\ demo.md --bibliography vault/H2G2.bib --citeproc --csl "https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl" -o vault/H2G2.pdf`
:::
---
### Why Zotero?
- Open source
- Community-developed Plugins
- OCR
See:
---
# Zotero
---
## Zotero GUI
- Where does it store its data?
- Collections and tags
- Ways to add new items
More info:
# Plugins
---
## Resources
-
-
-
-
:::notes
I migrated the mdnotes docs back to GitHub pages using Docusaurus (equal parts of blame go to the Discord server and GitBook for being horrible).
The "old" GitBook docs originally in the presentation are here:
:::
## Installing plugins
`Tools`>`Add ons` and drag and drop the three `xpi` files.
# Zotfile
---
## Why do you need Zotfile?
- Manage your attachments
- Extracting annotations
---
### Managing attachments
Renaming using wildcards, a few examples:
> - `%a` - last names of authors.
> - `%y` - year (from Date field)
> - `%j` - name of the journal
> - `%t` - title. Usually truncated after : . ?
> - Optional wild-cards mean that `{-%y}` only includes the separator `-` in the filename if `%y` is defined.
Full list of wildcards:
---
### Extract PDF Annotations
- Settings to customize the formatting are in the hidden preferences. You can get there by opening `Settings > Advanced > Config Editor` and then filtering by `pdfExtraction`.
::: notes
My settings:
- extensions.zotfile.pdfExtraction.colorAnnotations: true
- extensions.zotfile.pdfExtraction.colorNotes: true
- extensions.zotfile.pdfExtraction.formatNoteTitleColor: ``
`
:::
---
# Better BibTeX
---
## Why do you need Better BibTeX?
- Unique IDs for your references
- Plain-text backup of your sources
- Integration with other tools
---
### Citekey management
- Format `[auth:lower][year][journal:lower:abbr]`
Full list of options:
---
### Exporting bibliography
- Right-click on selected items/collections and choose `Better _____`
---
### Quick Copy
You need to look in two places:
- Zotero `Edit > Preferences > Export`
- Better BibTeX settings `Edit > Preferences > Better BibTeX > Citation keys > Quick copy`
---
### Citekey wildcard for Zotfile's renaming rules
Now it's possible to use the `{%b}` wildcard for renaming in Zotfile:
- Example: `-` would use the renaming rule `{%b-}{%t}`
---
# Mdnotes
## Why do you need Mdnotes?
- Exports to markdown
---
### Basic configuration
- Naming convention
- Single vs Multi File
![](mdnotes-file-config.png)
---
### Templates
- Which ones do I use?
![](mdnotes-templates.png)
- Default templates:
::: notes
My templates:
I've mixed and matched templates from many places, but these are the ones I currently use.
:::
---
### Placeholders and wildcards
Templates use `{{placeholders}}` to fill in the data, by default a placeholder has this format:
```
{{bullet}} {{field_name}}: {{field_contents}}
```
::: notes
- Adding the placeholder without customizing should be enough
:::
---
### Field customization
#### Where?
1. `Preferences > Advanced > Config Editor`
2. Filter for `mdnotes.placeholder`
The default preference for the `{{tags}}` placeholder looks like this:
```
{"content":"{{bullet}} Tags: {{field_contents}}", "field_contents": "#{{content}}", "link_style": "no-links", "list_separator": ", ", "remove_spaces": "true"}
```
#### More info:
- Zotero fields:
- Zotero `itemType`s:
::: notes
Adding placeholder for journals? `{{publicationTitle}}`
:::
---
### Field customization
![](mdnotes-custom-field.png)
![](mdnotes-custom-field-exploded.png)
---
#### Examples
Customizing the tags (`extensions.mdnotes.placeholder.tags`)
- Formatting them as `#zotero/`
```
{"content":"{{bullet}} Tags: {{field_contents}}", "field_contents": "#zotero/{{content}}", "link_style": "no-links", "list_separator": ", ", "remove_spaces": "true"}
```
- Formatting them as links:
```
{"content":"{{bullet}} Tags: {{field_contents}}", "field_contents": "{{content}}", "link_style": "wiki", "list_separator": ", ", "remove_spaces": "false"}
```
---
### Custom fields
Examples:
- For `extensions.mdnotes.placeholder.Bethselamin`:
```
{"content":"weird Planet from {{field_contents}}",
"zotero_field":"citekey"}
```
- For `extensions.mdnotes.placeholder.Earth`:
```
{"custom_content":"Mostly harmless"}
```
::: notes
Add this placeholders to a template:
```
{{flabbergabble}}
{{Bethselamin}}
{{Golgafrincham}}
{{Earth}}
```
yaml collections from Cat's post:
```
{"content":"Collections: \n- \"{{field_contents}}\"","zotero_field":"collections","link_style":"no-links","list_separator": "\"\n- \""}
```
:::