Thanks!

1. […] I feel like it should be possible to remove the older note

We'll think about that. It's tricky, since there's nothing special about the note — as you say, you can create multiple, or drag one in from another item, or copy and paste. But maybe we can store a hidden property on the note that gets cleared when edited and provide a quick way to update if there's a single such unmodified note under an item.

2. I think the "All Notes" view needs rethinking. I have hundreds of notes from across my library with no way of searching or filtering them and it takes up the lion's share of the right pane. This doesn't seem right.

Right, so, our thinking on this is that "All Notes" basically serves two purpose: 1) to let you quickly pull up a recent note you were working on (since it's sorted reverse chronologically) and 2) to provide the logical scope for the search bar so that you can pull up any note in your library. In that way, it's much like the root view of a library — in a large library, it's probably not particularly useful on its own, but it's a place you can go to search/filter your whole library. And since we know people have thousands of notes, we only show the seven most recent ones. (There's a button to show all if you really want to scroll through them, but you don't need to press that to use the search bar.)

An analogue here would be the left-hand pane in the Notes app on macOS. Technically you can scroll through every note you've ever taken, but really it's just there so you can click a recent one or search against the full list.

We do plan to add many more filtering options — right now the filtering is very basic. Are there specific ways of finding notes you would find useful there?

3. For the note editor -- would it be possible to bring back source view?

Short answer: probably not. ProseMirror isn't an HTML editor — it's object-based, and while it gets serialized to HTML on save for compatibility with TinyMCE, the HTML is much less human-friendly (large chunks of embedded data for annotations and citations) and exposing it risks corrupting what's there. We can talk about whether there might be some way to expose some sort of sanitized view that could be combined with the internal data, but that may be tough to do safely.

There's still a lot of note functionality we need to bring back to this version, though — colors, superscript/subscript, tables, alignment, and more. So don't be alarmed if something you use is absent.

4. As I was messing around, I realized that I found it difficult to find my way back to the item in the library. Would it be possible to implement a "Go to Note in Library" function, so that one can do that (and also the item itself). I imagine people will work on multiple pdfs and accumulate these tabs, and they may want to have an easier way to find their way back to the item from the pdf tab (under My Library, I assume, since the item may be under multiple collections).

5. One reason I was trying to go back to the item is to delete the note itself. I could not find a way to delete it from the pdf tab. A Delete button there will also help get rid of a note from an incomplete set of annotations and the user may recreate a new, complete one simply in two steps without changing tabs (solves case 1 above).

Regarding All Notes, I think the appearance when there are no item notes is kind of distracting and jarring, especially in Stacked View. Could there be more empty space given to an empty Item Notes section?

Related to 3., I would find a lot of use for a Markdown view. In RStudio for example, I switch back and forth between the Markdown and ProseMirror views really often. The biggest help for my typing habits would be being able to enter text formatting using markdown entry (eg, **a** for bold, # for headings, etc.).

6. I frequently email PDFs by dragging the attachment item from Zotero. It would be really nice if there was a prompt asking if annotations should be included when doing that.

7. How is the citation style for citations in notes controlled?

By distracting I just mean, it’s not clear immediately that there are 2 sections and that All Notes is all of the notes in the library. A clearer distinction between these sections would make it easier to understand what they are each for. Relabeling “All Notes” to “All Notes in My Library” might help too.

Re: 6. I’m guessing that a setting to automatically export annotations on a drag wouldn’t work then either? Maybe a permanent icon for this in the right pane for the attachment icon might be workable?

Re: 7. Got it. I don’t think the citation style is important, but I expect this to be a mild source of confusion. We will need an FAQ page explaining that the citation style will be set when the note text is inserted/copied into a word processor document.

@dstillman in the All Notes view, would it be possible in future versions to untether notes from their sources and show them separately, for example, view only notes including a particular word in the list? currently all notes for a particular item appear together.

Edit: Never mind, they are untethered! This is amazing, it is much easier to work with notes in this interface than in the main Zotero interface.

When I have a PDF open in one tab with the note editor open, if I open a new PDF from My Library, the existing note editor stays visible in the new tab with the new PDF.

Yes, that's by design. The Notes pane persists between tabs, so you can take notes across more than one PDF. The Item pane is specific to the PDF you're viewing. (We tried variations where child notes were editable in the Item pane and remained contextual, but it ended up being too confusing to have notes in too many places.)

I don't see a way to delete a note from either the notes list or the note editor view.

That will be possible from the notes list soon.

@enozkan: It wouldn't work for Zotero annotations to be saved to the original file. A lot of reasons: it would result in extra file uploads/downloads, it would be much harder/slower to do on web/mobile; since Zotero still supports externally created annotations, it would result in all sorts of issues reconciling changes made to the annotations by external readers (external readers stripping identifiers from the mirrored annotations, conflicts between the two different versions of an annotation, concurrency issues from open files). It would just be a total mess.

If disk space were no issue, someone could create a plugin that maintained a one-way mirror of PDFs with embedded annotations whenever the internal annotations changed (and, for the dragging issue specifically, overrode the drag functionality to use that version of the file).

@enozkan: We don't have to deal with reconciling changes now because the external annotations are read-only. In a future version we may support transferring annotations one way or another and deleting on the source side — importing annotations from a PDF and removing them from the file, or vice versa — but that's likely to be the only option (and, e.g., you'd lose Zotero tags on the annotations if saving to the file).

@dstillman I am not understanding exactly what the concerns are, but I don't need to. I trust you guys can see all the issues. Thank you for another excellent improvement.

On the confirmatory side, (1) I opened an attached pdf and annotated it in Acrobat Pro, (2) saved it in Acrobat Pro, (3) opened it in Zotero using the new pdf viewer, (4) added a new annotation, (5) saved it from the new pdf reader using "Save As", and (6) replaced the original pdf in the storage folder. This worked fine beautifully; no issues. The updated pdf opens in the new pdf reader with both annotations. So, if I choose to annotate my pdfs (including those with previous annotations) in the new pdf reader, I can do that and manually replace the file in the storage folder. Excellent!

Edit: I do not want to give bad advice to others, though. The new file has both annotations as read-only, and you have an extra for the one created in the new pdf reader (which is saved in the library, I assume). So this workflow should not be used (and wouldn't be endorsed by the developers rightfully so). For saving your annotations as standard pdf annotations, or quickly sharing annotated pdfs with others, there may be other ways.

> There's still a lot of note functionality we need to bring back to this version, though — colors, superscript/subscript, tables, alignment, and more. So don't be alarmed if something you use is absent.

That's excellent - looking forward to that!!

A few comments

(1)

Also, good that the file can be exported with the annotations using save-as.
(A) It wasn't clear to me that it would save with annotations - might be good to indicate somewhere.
(B) I wonder whether there could be an "attach duplicate with embedded annotations" or similar, that creates a 2nd attachment with the annotations baked in?

(2)

Overall, I would love more keyboard shortcuts (or a way for Zutilo to generate them). It would be nice to have keyboard shortcuts for hiding panels, but above all, I would love keyboard shortcuts for the tools (maybe 1/2/3?) and colours (r/g/b/??).

(3)

I assume that while we cannot drag out of Zotero, we can drag annotated PDFs between libraries, right?

As per other thread:

[removed duplicate comments — D.S.]

Thanks @dstillman !!

That's excellent - looking forward to that!!

I'd actually remove the remaining two comments from the other thread to move them here. Here they are again:

(4) Would love an option to add turn all PDF-annotations into a note each. That note would need to start with the text of the annotation so the initial text of the note can be seen in the Zotero middle panel. That note would be tagged with the tags added to the note in the PDF. (Cudos for adding tags to individual annotations!) This would make a quick qualitative analysis of the PDF document / extracting key quotes really simple. Would love to have this.

This could also check existing notes for exact duplicates and not recreate them, avoiding needless duplication.

(5) ZotFile-type customisation of the extracted text. I've got my ZotFile set up so that it uses the colour of the PDF-annotation to highlight part of the Zotero-note (e.g., the reference). Will it be possible to customise the text of the Zotero-note in any way (as you can with ZotFile)?

What I would love here is (customisation):
(a) Show the user name who made the annotation in the Zotero-note. (User would be the Zotero user or the user embedded in the PDF, depending on the type of annotation.)
(b) Show the highlight colour and the highlight colour name.
(c) Show the Zotero Item key for the PDF and for the parent item.
(d) Let the user customise character-based separators between those parts, so notes can be further processed.

For example, one could then do this (where "⟦Note:" is arbitrary markup chosen by user):

"Extracted text." (Author, Year, p. X) ⟦Note: ABC⟧⟦parent:123:ABC⟧⟦key:456:DEF⟧⟦Color:#FF0000:Red⟧⟦Tag:XXX⟧⟦Tag:YYY⟧⟦User:ZZZ⟧

or even

⟦text⟧"Extracted text."⟦/text⟧[ref⟧(Author, Year, p. X)⟦/ref⟧ ⟦Note: ABC⟧⟦parent:123:ABC⟧⟦key:456:DEF⟧⟦Color:#FF0000:Red⟧⟦Tag:XXX⟧⟦Tag:YYY⟧⟦User:ZZZ⟧

(The parent/key def seems to be present in the 'data-citation', but would be helpful to have a way of showing them in the plain text.)

I know the above adds more characters etc, but we have a way of 'onward processing' of the notes (by copy/paste), and it would be really good to have this.

Btw. I really love the way that you can drag paragraphs around in the note editor, that's very cool.

@Jes.Mullins:

I don't have an option to choose. I click the icon and it displays both.

To be clear, I meant "choose" in that you can open either item notes or standalone notes from the same place. They're notes either way, and they both need to open in a note editor.

A different tab (I mean functioning the same way parent item does) in the pane keeps things clean.

We went through multiple revisions of the design where child notes were in a separate pane (generally the context-specific item pane), but it ended up being far too confusing to have multiple note lists and multiple note editors, with different tab-pinning behavior, as you switched between panes and tabs.

The only use case I can think of for needing "All Notes" is if when reading an article I think to look up related issues/comments/notes from other articles. Otherwise I have no need of it when viewing an article

That's understandable. I think it will depend on people's workflows. If while viewing a PDF you would only ever work on child notes, I can see having other notes show up there being distracting.

Much of the functionality of the new note editor is based around the idea of using standalone notes further into a draft as you combine material from various sources, and the All Notes section — and the pinning of notes between tabs — is meant to address that use case. But I understand that not everyone will want to work that way, or may want to do that part outside the PDF reader.

We'll see what we can do here. Thanks for your feedback.

Would it be possible to view standalone notes in tabs?

Yes, this is planned. In the meantime, you can open notes in separate windows from the library view.

Is there going to be an option to hide or shorten the citation that is shown after an annotation in the notes? […] For me the best option would be to show just the page number, and that to work as a link to the specific page in the PDF.

Notes are designed to be combined into a larger standalone notes, so if we did this, it would have to be conditional based on the view. We could consider showing only the page number 1) when viewing a child note, 2) when viewing it in the library view or the PDF reader with that specific PDF open, and 3) when there are no citations for other items in the note.

Would it be possible to have the quotation marks as optional when copying annotations into notes? I prefer not to have them.

I don't see us doing that. This is a situation where we know the specific context of the text, and we want to help people avoid accidental plagiarism or misattribution.

(Quotation marks are currently added when copying text from the PDF to anywhere, though, including fields, and that's a bug.)

I strongly agree with @adamsmith 's comment about updating annotations rather than creating a duplicate. Though I have nothing to contribute to the discussion about whatever wizardry you'd need in order to implement it...

If disk space were no issue, someone could create a plugin that maintained a one-way mirror of PDFs with embedded annotations whenever the internal annotations changed (and, for the dragging issue specifically, overrode the drag functionality to use that version of the file).

Now that some time has passed, has anybody created a plugin like this? It would be a very useful feature in my workflow if i could take advantage of both the native annotation tagging in Zotero’s PDF reader and the nested folder organization of Zotfile.