frianasoa/ze-notes

Zotero plugin for note management. Helping you visualize your notes and annotations efficiently.

Ze Notes

Now works with Zotero 7 Beta.

Description

ZeNotes is a Zotero plugin that will help you manage and visualize your notes. It is helpfull if you intend to make a systematic review directly on your Zotero using notes and pdf annotations. This tool will help you organize your notes on Zotero. It will show you on a table what you have been writing. You can edit your notes right on the table or add new notes. On the latest versions, you can add translations of your notes using Google or DeepL. You can also apply a generative AI prompts (Bard and ChatGPT for the moment) to a cell, a row, or the entire table. These actions are also available right in the pdf reader of Zotero.

How to migrate your preferences to v0.4.* and later

• After installing the plugin, restart Zotero (This will import your preferences from previous versions)
• Select the collection you are working on
• Head to ZeNotes > Settings
• In settings, scroll down to "Load and save"
• Click on the dropdown and choose the preference you want to apply to the current collection
  • Preferences from Zotero 6 are imported automatically and their names will start with Z6. "Z6 default" will hold your last preference on Zotero 6.
• Click "Import preferences" to apply the selected preference to the current collection

Limitations & bugs for current version

• "Show annotation" does not open the pdf at the page with highlight on Zotero 7.
• If it is of concern for you, please stay on Zotero 6 until it's resolved.

Instructions

Install

• Head to the release page: https://github.com/frianasoa/Ze-Notes/releases/
• Download the latest version of the ".xpi" file. Please right click and "save as" if your browser tries to install it and fail.
• Open your Zotero. On the menu, click “Tools → Add-Ons” to open a window.
• Drag the .xpi file for the plugin onto that window.
• Alternatively, you can click on the clog on the top right corner, then click "Install Add-on From File", choose the file and open.
• Restart your Zotero.
  Form more on Add-ons see this page https://www.zotero.org/support/plugins

Use

Adding notes

• Add notes to an entry

• Or add annotations directly on an attached pdf file [You need to use Zotero pdf reader if you want to use annotations].

• To each note or annotation, add a tag.

Displaying notes

• Right click on a particular collection or on "My Library". Then, click "ZeNotes - My notes in collection" from the context menu.
• Alternatively, select a particular collection or "My Library", then on the menu "ZeNotes > Notes".
• A table should be displayed.

Edit notes

• You can edit your notes normally in Zotero or right click on an item in the table to see your options.

AI Assisted paraphrasing

• Go to ZeNotes > Settings > Global Settings > AI API Settings

• Insert your API Key

• Display your notes and right click on an annotation. The menu "Paraphrase annotation" will be available. Choose Bard or ChatGPT depending on the API key you have. It will paraphrase the excerpt selected in the PDF file.

• Here are some links to access Google Ai Studio (Bard) [Can be used for free so far] [If it does not work, search the internet. These things move so fast]. https://ai.google.dev/pricing https://makersuite.google.com

• For Open Ai (ChatGPT), head to https://platform.openai.com/api-keys. You will be asked to sign up. If you have never signed up (ChatGPT on the web included), you may get some free credits at the beginning (they expire). Otherwise you will need to buy some credits to be able to use the API. Please be warned that Open AI credits expire after 1 year if not used (at the time of writing. Please always check.). Do not try to create multiple accounts using the same email and/or mobile phone, you might get banned.

• For DeepL API key, head to https://www.deepl.com/account/plan after you sign up. They will ask you for your credit card details even for the free plan.

Choose which tags or field to show on the table

• To open preference, go to menu "Edit > Preferences" of the ZeNotes window. Alternatively go to menu "ZeNotes > Settings" of the Zotero main window.
• Select the tags you will be using as columns. You can hide the ones you do not need.
• You can choose the tags on which you want to sort the results. Click on the icon a->z or z-> to change how you want to sort.
• The current layout is automatically saved for the current (selected) selection.
• Click "OK" when you finish and the table will reload.

API settings

Extra menus are available for each API you set (contextmenu: when you write click on the table or on an annotation in the pdf reader). For Bard and Open AI, you can set the models you want to use. You can set the maximum token used for OpenAI as well.
The plugin has simple default prompt for each action. You can set your own in "AI custom prompts". Remember that when you change them, the menus would mean something completely different from the label (If you change paraphrase prompt into something else for example).
Last, you can set the language for Google and DeepL translation the label of the contextmenu will change accordingly.

Other settings

These global settings apply to the plugin as a whole.

Font settings was added. You can use this to zoom in and out of your table with the shortcut "Ctrl + Mouse wheel" or "Ctrl + Plus/Minus"

Use cases

How to start a systematic review of the literature?

1. Create a folder (collection) to add all the papers you want to review (you can also use an existing folder).
2. Add notes to each entry of the folder. It is also possible to add annotations directly inside a pdf attachment.
3. To each note or annotation, add a tag according to its content (e.g. Objectives, Methods, Results, Discussions, Comments, ... ). If you do not add a tag, the note or annotation will be tagged "Untagged".
4. Right click on the folder you work on and open "ZeNotes - My notes in collection" to see all your notes in the current collection. All your notes will be shown in a table with the tags as column headers. You can choose "vertical table" if you want to display them as row headers instead.
5. You may right click on the table cells to see what actions are available (Edit, remove columns, etc, ...). You can also drag and drop the headers.
6. Go to tools and settings to control the columns (tags) you want to show or hide. You may also sort the results. The setting you choose will be saved automatically for each collection.
7. Use Google translate or DeepL to translate your annotations. You can apply a generative AI prompt to each cell as well.
8. Export your notes to MS Word, Excel or CSV format.

Disclaimer

Before utilizing any of the API introduced above, please carefully review the terms of service, usage guidelines, and agreements associated on their official websites.

ze-notes's Issues

[Request] Add support to show images marked directly with "Select Area" Tool

Hi, thanks for this incredibly amazing plugin!! I'm wondering if it is possible to show note image selected using Zotero "Select Area" Tool directly in the table (currently it only shows a "" instead of the selected image). (I'm using Zotero7 on macos.)

The workflow is shown below:

Can it be displayed vertically?

Can you add vertical browsing?

The effect is shown in Fig.

Can we NOT displaying titles of notes in the table?

Thank you first for the excellent extension that offers me a novel way to manage and collect INFOs scattered in numerous notes within my Zotero base.

Here, I wanna know is it possible to NOT displaying the title of all collected notes in the summary table. In practice, I both need a title to label my note and directly copy the contents in a table column to another. This two needs, however, clashes each other if the titles are included in the table: what we want is usually the content IN the note, not the title (which is just the indiciator for me to locate the target note).

Displaying titles in the summary table, as a result, may pollute the summarized contents so that the user has to spend time on removing these them before formal use, and it is an uncessary loss of efficiency. I think if we could make the titles (at least the first H1 header) disappear, the workflow would be more fluent.

Thank you for any potential response! Anyway Ze-Notes is still an excellent extension and I'll keep using it.

What is the tag "other"

This tag exists in some collections, does not exist in some collections,but i don't have this tag.

Pressing ctrl only makes the text enlarge when ctrl+c copies the text.

Thank you for your continued interest in this project.

Pressing ctrl only makes the text enlarge when ctrl+c copies the text.

The following are suggestions for modifications.

Would it be possible to add a markdown file export format that includes backlinks?

Not displaying notes

Hi , thanks for the excellent plug in , very useful ,
The only issue is that I can't open the notes with this warning:

notes.init 1: Error: getNotes() cannot be called on items of type 'note'

SUPER Wow! And, Some Files Not Working.

Hi,

I got the plugin to work! 💯 Yay!

Here's what I'm seeing. I tested it using five different PDF files.

Three worked fine - and WOW! That TABLE and what it CAN DO! That's the DREAM. Your work is amazing!!!

Trouble I'm having is that with two files, the system only loaded the table headers of the existing tages, but left the columns all blank.

So, 3 of 5 PDF files worked perfectly.

The other two - though they HAD annotaions, the table only loads the headers / tag names. No highlight content / columns.

Trouble for me is, the 5th file is REALLY the main file I need to work with. And, files like that.

It's original research, so I can't share it. But, I've uploaded the 4th file, too - it was just an NVIDIA tech guide, but it showed the same problems.

Please can you take a look at the file and see if you can understand what's happening? I REALLY need Ze-notes to get a BIG project done. Need your help, please.

nvidia-smi.1.pdf

Multi-label bug

If a note has multiple tags, Ze-Notes displays only the contents of the first and last tags, not the middle tags. And the content will be displayed repeatedly.

Add Horizontal Rows Based on Table of Contents and Definable

Hi, frianasoa!

The plug in is SOOOOO useful for literature review. THANK YOU for working so hard to make something so amazing. Right down to a slider for the colors of the highlights. GREAT stuff!

I have an idea. Tell me what you think. There's one feature I feel would be a HUGE help. I'm stuck with reading some really abstract books over the next few years...the arguments are hard for my poor wee brain to follow.

By and large the authors will make their points in each chapter - so that they will present and wrap concept by concept as the chapters go along.

Is there any way we could add horizontal rows to the table?

My first idea is to inherit the chapter headings in the table of contents. Since that's already in the file's structure I was thinking that would be less troublesome for you.

That way, there'd be a visible division within the annotations related to each chapter.

Ideally, it would be great if we could insert our OWN divisions, as many times in my own reading I'll find that the TOC either omits lots of sub headings, or I just get into 10 or 20 paragraphs that define a main idea well. So, have the TOC as auto-inserted rows, and then have the ability for us to define our own rows if needed.

In using the plug in, I did notice a feature to add a row, but I couldn't figure out how to use it.

With horizontal rows based on the chapter headings inside the table, it would make the reviews of the annotations REALLY easy and increase the efficiency.

How does that sound?

Sincerely,

Trip

Zotero 7 support

Could this awesome extension support Zotero 7?

Allow Unlimited Size of Tags & Let Users Define Column Width

Hi,

I need to be able to make some fairly long tags - ideas that occur to me which I may or may not use, and don't really boil down to two or three words.

I've done that with one academic work this week - using PRETTY long tags - and the result as to break the table.

That is, the columns all stayed a fixed width, but the first row with the tags became very tall.

And. there was no way to get to the second row with the quotes.

Basically, it was a full screen showing ONLY VERY TALL COLUMNS of just the tags row. You could scroll up and down that tall tags row, but you could not get to the highlight themselves.

Please can you enable the tags to have no limit on characters?

And, please could you allow users to define the width of columns?

Sincerely.

Triplu

Unable to display Chinese author name.

Thank you for creating this incredibly useful plugin. I want to express my gratitude. However, I have come across a bug where author names are displayed correctly for English documents, but not for Chinese ones. I would appreciate it if you could let me know what additional information is needed to address this issue.

Can you display pictures normally?

The picture here can't be displayed normally. If it can't be displayed normally, can you use a symbol to indicate that there is a picture here? Otherwise, the picture can not be displayed, and it occupies a large display area.
The problem is shown in the following figure

[Bug] an error occur when there is a standalone note.

When there is a standalone note in the selected collection, an alert would occur.

Is it possible to ignore standalone notes in the collection?

open Tab by loadURI get error

NS_ERROR_XPC_BAD_CONVERT_JS: Could not convert JavaScript argument arg 0 [nsIWebNavigation.loadURI]

try this.
change

     Ui.iframe.loadURI(url, {

to

      const iframe = Ui.iframe;
      try {
        iframe.loadURI(url, {
          triggeringPrincipal:
            Services.scriptSecurityManager.getSystemPrincipal(),
        });
      } catch (e) {
          ztoolkit.log("loadURI 错误修复了吗？");
        iframe.src = url;
      }

[request] Add "show all" and "hide all" in tag settings

I can't say how grateful I am for you developing this. No need for me to use Citavi or they to figure out ways to work around in Obsidian/Notify etc.. What you did is amazing.

As you can see in the image, my settings page looks different than what you have on the notes. (Using macOS Sonoma 14.1.1 and Zotero 7.0.0-beta.53+969031a37)

So I was wondering if you can add a hide all option to the tag display area, so I don't need to go through giding them individually.

Can you dd a blank column to make the table more standardized?

Thank you for making such a thoughtful tool.
When exporting the table, can you add a blank column to make the table more standardized?

| id | title |
| --- | --- |
| 11 | 222 |

​