Exporting Notes, Annotations, With Tags, Limitations, HELP!

Hello, working on a literature review and critical analysis for masters thesis. Had such high hopes for using zotero for more than just citations and the bibliography this time around! But after laying all the groundwork and doing much annotation and preparation to synthesize in Zotero, I HAVE HIT A WALL! and am really disappointed and upset.

I used tags and subcollections to categorize and sort my articles and resources. So that I could synthesize findings in chunks (because unlike excel's filtering, you can't exclude tags or filter very well from the main screen... Please make this better!!!)

I ALSO went to the trouble of tagging MANY of my annotations so that I could sort them by topic or application or where I wanted to put them in my paper to synthesize them by groupings later.

Now I have been struggling to find a way to even batch and export just notes or just annotations into another program to sort and synthesize my notes and annotations using the groupings I created using subcollections and tags (I am using text editor since I am not as far down the rabbit hole to need obsidian or other special software).

The only work arounds I have found to to select the subcollections contents command+A and right click and generate report. This at least shows the tags for the article and the annotations in the notes (but if you made annotations and did not generate a note you may be out of luck). Also the report is bulky as it contains all the info for the work, i.e. title authors, TOC etc. so is not a ideal way to consolidate notes.

Also, here there are some limitations to having tagged your annotations:
1. Tags added to annotations are not carried over with the annotations to the notes when you "generate the note from annotations." Maddening
2. Tags assigned to annotation are not automatically assigned to the parent item or article in which the annotations are made. DUMB
(I mean if you give us the option to tag contents of a source, at least give use the option of having the parent item reflect the tagging)

So the other work around I found, is to again select a subcollection, filter to the ones I want to focus on, select all, right click, and "generate a note from annotations."

AMAZING! It puts the title at the top, lists only the annotations and comments below with a parenthetical reference to the work...

But again, NONE of the tagging on the individual annotations is carried over!

To make it EVEN MORE frustrating, there is a place where the annotations' tags could carry over and be linked just to the note for that file, and not even to the whole parent item (the little area at the bottom of the note that has a place for tags and related... but do the tags assigned to the annotations go there? NO! of course not!

Ok, so obviously there isn't a way to group these and synthesize in another app using the tags. So I set out to try to find a way to at least be able to search for those annotations that I made and that I have given certain tags...

From the main screen in the tag selector, tags assigned only to annotations (and not to parent items) show up! *Glimmer of Hope*

But when you select them and expand the parent item, it merely highlights the PDF file for the article. (Of course, because the tags aren't in the notes).

When you go to the annotations pane, the only way to select those annotations is by the color or by clicking the tag given...

There is no search box to type them, which is annoying to scroll through a lot of them). There is a search bar at the top! But it only searches the text highlighted to make the annotations and any comments entered. It does not search the tags!? WHY?

Unlike the notes pane which allows you to modify and search and toggle between notes for that item that is open in the main pane, and those for other works, even searching for words and modifying other notes etc. The annotations pane only lets you search the annotations for that single work. BAHHHHH

So in summary, I spent a great deal of time tagging hundreds of annotations to help me and efficiently create mind map, comparison table, and streamline the synthesis part of my literature review and critical analysis only to find out that Zotero offers these features but not a way to actually use them effectively!? WHY ?! I am so disappointed and frustrated!

Please help if there are work-arounds I missed, especially don't require me getting and learning a new piece of software!
Thank you!

Additional Feature Requests:
Can there please be a column for has annotations? There is one for has a note, and if added this would allow you to make ensure that you haven't' forgotten to generate a note for those you have annotated .... just saying.

Also from the main pane, it would be amazing to have filtering ability like in excel, i.e. those with and without attachments, with and without notes.

And please for the love, you can't exclude tags! By adding an AND/OR/NOT feature for the tags used would be AMAZING. I have so many subcollections I had to create to weed through collections of those with this tag but not with this tag to get counts and hone my groupings.... adding this feature and filtering from the main screen... Would make this so much better!
  • (Much easier to answer succinct posts than frustrated rants)
    For your main issue, see https://forums.zotero.org/discussion/comment/403053/#Comment_403053 for
  • Thank you , what you shared helped with some of the issues.
    (And yes I know it was long but was trying to show all the work arounds I had had tried to use to no avail, so that if I had missed something on one of them instructions might be given.)

    The code in the link you shared and related links I read about the note templates are mainly about the highlights. If you are using the square tool to take the equivalent of screenshots which get pulling into the notes just like the highlighted annotations, the codes used don't seem to apply. So if I have tagged and commented on a annotation using the square tool the comment doesn't get formatted the same way as it it were a highlighted item. Also, the tags are not added. This is part of what I am try to use because much of what I tagged were figures diagrams and tables.

    Thanks so much!
  • I mean, there's not much to say here other than that it's a good idea to test that a tool can handle the very specific workflow you have in mind before committing huge amounts of time to it?

    The PDF reader was introduced in Zotero 6 earlier this year. It has a huge amount of functionality, but a lot more is still to come.

    Annotation tags can currently be used in a few ways:

    - You can filter annotations in the PDF reader sidebar.

    - You can search or filter for attachments in the library view.

    - You can create a list of tags for highlight and note annotations added to notes if you modify the note templates. (There's currently no note template for image annotations, so that's not possible for those annotations.)

    A lot more will be possible in the future, but we get hundreds of feature requests every year, and we can't promise when any particular feature will be available.

    The ability to include annotation tags when adding annotations to notes without modifying a template is planned.
    There is a search bar at the top! But it only searches the text highlighted to make the annotations and any comments entered. It does not search the tags!? WHY?
    Because it hasn't been implemented, and you're the first to mention it? If you want a feature, you can just ask for it — you don't have to rant about it in all-caps. Anyway, we'll add this.
  • Ipe
    edited November 23, 2022
    Please, have a look at this:

    It can both transfer tags from an annotation to a note and collect annotation highlights marked with a certain tag.
  • Thank you both for your help!

    I apologize for conveying my frustration. This project is overwhelming and overdue and I had just discover I had spent a week solid tagging things to streamline the process only to find what I had posted about.

    I did not realize the PDF annotation tool was that new! Prior to this year have really only used it for citations and generating works cited. This is also my first experience with software that is user modifiable using code. Other than extensions for chrome and word, I am not super experienced in adding on things to software's capacities. And I haven't used html since undergrad, which I hate to admit how many years ago that was!

    ***Follow up question:***
    Since there is no note template for image annotations, is there perhaps a work around to convert tags on those image annotations to comments so that they are reflected (and searchable) when I generate and export notes?

    Thank you again!
  • Not sure about any plugins, but there's not currently any built-in way to get tags from image annotations into notes, no.

    But here's a quick script you can run in Tools → Developer → Run JavaScript to add image annotation tags to the comment field for any selected items in the items list:

    for (let item of await ZoteroPane.getSelectedItems()) {
    let bestAttachment = await item.getBestAttachment();
    if (!bestAttachment) continue;
    for (let annotation of bestAttachment.getAnnotations()) {
    if (annotation.annotationType == 'image') {
    let tags = annotation.getTags().map(x => x.tag);
    if (tags.length) {
    let str = "";
    if (annotation.annotationComment) {
    str += annotation.annotationComment + "\n\n";
    str += '#' + tags.join(', #');
    annotation.annotationComment = str;
    await annotation.saveTx();

    I wrote this quickly, so you should temporarily disable auto-sync in the Sync pane of the preferences and make a backup of zotero.sqlite in your Zotero data directory before running this, and make sure it does what you want before re-enabling sync.
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